Compositions comprising semaphorins for the treatment of angiogenesis related diseases and methods of selection thereof

ABSTRACT

A method of selecting a semaphorin for treating cancer in a subject is disclosed. The method comprises determining an expression of a semaphorin receptor on tumor cells of a tumor sample of the subject wherein an amount of the semaphorin receptor is indicative of the semaphorin suitable for treating the cancer in the subject. Methods of treating angiogenesis, kits for treating cancer and pharmaceutical compositions comprising semaphorins are also disclosed.

RELATED APPLICATIONS

This Application is a National Phase of PCT Patent Application No. PCT/IL2008/001307 having International filing date of Oct. 2, 2008, which claims the benefit of U.S. Provisional Patent Application Nos. 61/071,560 filed on May 6, 2008, 61/071,053 filed on Apr. 10, 2008, 61/006,496 filed on Jan. 16, 2008, and 60/960,910 filed on Oct. 19, 2007. The contents of the above Applications are all incorporated herein by reference.

FIELD AND BACKGROUND OF THE INVENTION

The present invention, in some embodiments thereof, relates to methods and compositions for treating angiogenesis-related diseases such as cancer, and methods of selection thereof.

The neuropilin-1 (np1) and the neuropilin-2 (np2) receptors were originally characterized as functional receptors for axon guidance factors belonging to the class-3 semaphorin (sema3) family. It was subsequently realized that the neuropilins are expressed by endothelial cells and by many types of cancer cells. It was also found that the neuropilins function in addition as receptors for several angiogenic factors belonging to the VEGF family and as receptors for the angiogenesis/metastasis inducing growth factor hepatocyte growth factor/scatter factor (HGF/SF), and that they function as potent enhancers of their pro-angiogenic activity.

Most of the sema3s, with the exception of sema3E which binds to PlexD1, bind to one of the two neuropilin receptors or to both. Neuropilins form spontaneous complexes with several members of the plexin receptor family. In these complexes the sema3s bind to neuropilins while the plexins function as the signal transducing elements. The four type-A plexins (plexins-A1 to plexin-A4) as well as plexin-D1 form complexes with neuropilins and participate in neuropilin mediated signal transduction.

Semaphorins sema3B and sema3F were also characterized as tumor suppressors whose loss contributes to the development of lung cancer [Tomizawa, Y., 2001, Proc. Natl. Acad. Sci. U.S.A 98:13954-13959; Xiang, R., 2002. Cancer Res. 62:2637-2643].

The identification of neuropilins in endothelial cells suggested that class-3 semaphorins may be able to regulate angiogenesis. Indeed, the class-3 semaphorin sema3F, a np2 agonist, functions as a repellant of endothelial cells, induces apoptosis of endothelial cells upon prolonged stimulation [Bielenberg, D. R., et al., 2004, J. Clin. Invest 114:1260-1271; Guttmann-Raviv, N., et al., 2007, J. Biol. Chem. 282:26294-26305] and inhibits angiogenesis and tumor progression in-vivo Mielenberg, D. R., et al., 2004, J. Clin. Invest 114:1260-1271; Kessler, O., et al 2004. Cancer Res. 64:1008-1015. The np1 agonist sema3A was also shown to inhibit in-vitro and in-vivo angiogenesis [Miao, H. Q., 1999. J. Cell Biol. 146:233-242. Bates, D., 2003, Dev. Biol. 255:77-98; Acevedo, L. M., 2008. Blood. 111:2674-2680]. Sema3E was also characterized as a repulsive agent that inhibits the invasion of PlexD1 expressing blood vessels into somites during embryonic development [Gu C. et al., 2005, Science 307:265-268].

In contrast, existing data suggests that sema3C functions as a pro-tumorigenic and pro-angiogenic agent [Herman J G, et al, Int. J. Oncol. 2007; 30:1231-1238; Banu N, FASEB J. 2006; 20:2150-2152].

The fact that neuropilins and plexins such as PlexD1 are also expressed by many types of tumor cells indicates that semaphorins may also affect the behavior of tumor cells directly. Indeed, sema3s such as sema3F and sema3B have been observed to inhibit the adhesion, migration or the proliferation of tumor cells expressing appropriate semaphorin receptors [Tomizawa, Y., 2001, Proc. Natl. Acad. Sci. U.S.A 98:13954-13959; Xiang, R., 2002. Cancer Res. 62:2637-2643; Bielenberg, D. R., et al., 2004, J. Clin. Invest 114:1260-1271; Nasarre, 2006, Neoplasia. 7:180-189]. In contrast, however, the cleavage product of Sema3E, was shown to be an inducer of tumor invasiveness and tumor metastasis [Christensen, C, 2005, Cancer Res. 65, 6167-6177].

SUMMARY OF THE INVENTION

According to an aspect of some embodiments of the present invention there is provided a method of selecting a semaphorin for treating cancer in a subject, the method comprising determining an expression of a semaphorin receptor on tumor cells of a tumor sample of the subject wherein an amount of the semaphorin receptor is indicative of the semaphorin suitable for treating the cancer in the subject.

According to an aspect of some embodiments of the present invention there is provided a method of treating cancer in a subject in need thereof, the method comprising:

(a) selecting a semaphorin for treating cancer in the subject according to the method of the present invention; and

(b) contacting cancerous cells of the subject with a therapeutically effective amount of an agent capable of upregulating said semaphorin, thereby treating the cancer.

According to an aspect of some embodiments of the present invention there is provided a kit for treating cancer, the kit comprising at least one agent capable of identifying a semaphorin receptor sub-type and at least one semaphorin.

According to an aspect of some embodiments of the present invention there is provided a method of treating a disease associated with angiogenesis in a subject in need thereof, the method comprising administering to the subject a therapeutically effective amount of a semaphorin selected from the group consisting of Sema3D, Sema3E and Sema3G, thereby treating the disease associated with angiogenesis.

According to an aspect of some embodiments of the present invention there is provided a use of a semaphorin selected from the group consisting of Sema3D, Sema3E and Sema3G for the treatment of a disease associated with angiogenesis.

According to an aspect of some embodiments of the present invention there is provided a pharmaceutical composition comprising as an active ingredient a semaphorin selected from the group consisting of Sema3D, Sema3E and Sema 3G and a pharmaceutically acceptable carrier.

According to some embodiments of the invention, when the semaphorin receptor comprises NP1, the semaphorin comprises Sema3A or Sema3D.

According to some embodiments of the invention, when the semaphorin receptor comprises NP2, the semaphorin comprises Sema3G or Sema3F.

According to some embodiments of the invention, when the semaphorin receptor comprises PlexD1, the semaphorin comprises Sema3E.

According to some embodiments of the invention, the agent is an antibody.

According to some embodiments of the invention, the determining is effected using an antibody.

According to some embodiments of the invention, the semaphorin is a class 3 semaphorin.

According to some embodiments of the invention, the class 3 semaphorin is selected from the group consisting of sema3A, sema3C, sema3D, sema3E and sema3G.

According to some embodiments of the invention, the contacting is effected in vivo.

According to some embodiments of the invention, the contacting is effected ex vivo.

According to some embodiments of the invention, the agent is a polynucleotide agent comprising a nucleic acid sequence encoding the semaphorin.

According to some embodiments of the invention, the semaphorin receptor is selected from the group consisting of Np1, Np2, PlexA1-4 and PlexD.

According to some embodiments of the invention, the semaphorin is sema3E.

According to some embodiments of the invention, the sema3E is a pro-protein convertase resistant Sema3E.

According to some embodiments of the invention, the disease associated with angiogenesis is selected from the group consisting of cancer, arthritis, rheumatoid arthritis, atherosclerotic plaques, corneal graft neovascularization, hypertrophic or keloid scars, proliferative retinopathy, diabetic retinopathy, macular degeneration, granulation, neovascular glaucoma and uveitis.

Unless otherwise defined, all technical and/or scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which the invention pertains. Although methods and materials similar or equivalent to those described herein can be used in the practice or testing of embodiments of the invention, exemplary methods and/or materials are described below. In case of conflict, the patent specification, including definitions, will control. In addition, the materials, methods, and examples are illustrative only and are not intended to be necessarily limiting.

BRIEF DESCRIPTION OF THE DRAWINGS

Some embodiments of the invention are herein described, by way of example only, with reference to the accompanying drawings. With specific reference now to the drawings in detail, it is stressed that the particulars shown are by way of example and for purposes of illustrative discussion of embodiments of the invention. In this regard, the description taken with the drawings makes apparent to those skilled in the art how embodiments of the invention may be practiced.

In the drawings:

FIGS. 1A-C are photographs illustrating the expression of sema3 receptors in breast cancer derived cell lines. FIG. 1A. Cells were grown to 80% confluency and lysed. Equal amounts of protein were loaded and separated on SDS/PAGE gels and blotted on nitrocellulose. Western blot analysis of np1 and np2 was performed as described. FIGS. 1B-C. Reverse PCR analysis of plexA1-A4 and plexD1 expression was performed according to the instruction of the PerfectPure kit using primer pairs specific to the different plexins.

FIGS. 2A-L are graphs and photographs illustrating the effect of the expression of different sema3s on the development of tumors from MDA-MB-231 cells. MDA-MB-231 cells were implanted in the mammary fat pads of balb\c nu/nu mice as described. FIGS. 2A, D, G, J. Western blot analysis of aliquots of conditioned medium derived from cells expressing the different sema3s. At the end of the experiment tumors were excised and photographed. FIGS. 2B, E, H, K. The average volume of the developing tumors was measured as described. FIGS. 2C, F, I, L. The average weight of the tumors at the end of the experiment was determined as described.

FIGS. 3A-I are graphs and photographs illustrating the effect of the expression of different sema3s on the development of tumors from MDA-MB-435 cells. MDA-MB-435 cells were implanted in the mammary fat pad of balb\c nu/nu mice as described. FIGS. 3A, D, G. Western blot analysis of aliquots of conditioned medium derived from cells expressing the different sema3s. FIGS. 3B, E, H. The average volume of the developing tumors was measured as described. FIGS. 3C, F, I. The average weight of the tumors at the end of the experiment was determined as described.

FIGS. 4A-F are graphs and photographs illustrating the effect of the expression of sema3A and sema3F on the development of tumors from MCF-7 and MDA-MB-468 cells. MCF-7 and MDA-MB-468 cells were implanted in the mammary fat pad of balb\c nu/nu mice as described. FIGS. 4A, D. Western blot analysis of aliquots of conditioned medium derived from cells expressing either sema3A or sema3F. FIGS. 4B, E. The average volume of the developing tumors was measured as described. FIGS. 4C, F. The average weight of the tumors at the end of the experiment was determined as described.

FIGS. 5A-E are graphs and photographs illustrating that different sema3s repel endothelial cells in-vitro and reduce the density of tumor associated blood vessels in-vivo. FIG. 5A: Control HEK293 cells infected with an empty lentiviral vector or HEK293 cells expressing sema3A, sema3D or sema3E were seeded on top of a monolayer of HUVEC cells as described in experimental procedures. The HEK292 cells were labeled with the fluorescent vital dye DIasp prior to seeding. Shown are composite pictures taken by phase and fluorescent microscopy. FIG. 5B. Control HEK293 cells infected with an empty lentiviral vector or HEK293 cells expressing sema3F, sema3G were seeded on a monolayer of PAE cells expressing np2 and plexA1 as described in the Materials and Methods. The HEK293 cells were stained with DIasp and photographed as described herein above. FIG. 5C. The average area of blood vessels per microscopic field was determined in sections derived from tumors that developed from control MDA-MB-231 cells or from MDA-MB-231 cells expressing different sema3s as described herein. Since the tumors that did develop from sema3A expressing cells were extremely small, the density of blood vessels in them could not be determined FIG. 5D. The average area of blood vessels per microscopic field was determined in tumors derived from control MCF-7 cells or from MCF-7 cells expressing sema3A or sema3F as described herein above. FIG. 5E. The average area of blood vessels per microscopic field was determined in tumors that developed from control MDA-MB-435 cells or from MDA-MB-435 cells expressing different sema3s as described herein above. No tumors developed from sema3G expressing cells.

FIGS. 6A-D are graphs and photographs illustrating that different sema3s inhibit the formation of soft agar colonies from MDA-MB-231 or MDA-MB-435 cells. FIG. 13A. Single cell suspensions of control MDA-MB-231 cells or MDA-MB-231 cells expressing different sema3s were seeded in soft agar as described herein. Colonies were allowed to form for 21 days. The colonies were then stained with crystal violet and microscopic fields photographed. The average number/field of colonies with a diameter exceeding 150 μm was then determined as described under experimental procedures. FIG. 6B. Photographs of representative microscopic fields containing crystal violet stained colonies that developed in soft agar from control MDA-MB-231 cells or from sema3s expressing MDA-MB-231 cells. FIG. 6C. The formation of colonies in soft agar from control MDA-MB-435 cells or from MDA-MB-435 cells expressing different sema3s was determined as described herein above. FIG. 6D. Photographs of representative microscopic fields containing crystal violet stained colonies that developed in soft agar from control MDA-MB-435 cells or from sema3s expressing MDA-MB-435 cells.

FIGS. 7A-D are graphs and photographs illustrating that expression of np1 in MDA-MB-435 cells enhances the growth of resulting tumors and sema3A abrogate the enhancing effect. FIG. 7A. A western blot comparing the expression of np1 in MDA-MB-435 cells infected with various combinations as depicted of a control lentiviral vector, a lentiviral vector containing the npl cDNA and a lentiviral vector containing the sema3A cDNA is shown at the top. The Average tumor volume as was measured during the experiment as described and is shown in the graph below. FIG. 7B. Photographs of tumors excised at the end of the experiment. FIG. 7C. The average weight of the tumors at the end of the experiment was determined FIG. 7D. The average area of blood vessels/field in tumor sections was determined.

DESCRIPTION OF SPECIFIC EMBODIMENTS OF THE INVENTION

The present invention, in some embodiments thereof, relates to methods and compositions for treating angiogenesis-related diseases such as cancer, and methods of selection thereof.

Before explaining at least one embodiment of the invention in detail, it is to be understood that the invention is not necessarily limited in its application to the details set forth in the following description or exemplified by the Examples. The invention is capable of other embodiments or of being practiced or carried out in various ways.

The semaphorins belonging to the class-3 semaphorin sub-family (sema-3s) function as axon guidance factors during embryonic development. Most of the class-3 semaphorins, with the exception of sema3E, bind to one of the two neuropilin receptors, which in turn form complexes with several members of the plexin receptor family. In these complexes the neuropilins bind the semaphorins while the plexins function as the signal transducing elements.

Semaphorins sema3B and sema3F have been characterized as tumor suppressors, whilst sema3F, sema3A and sema3E have each been attributed an anti angiogenic function.

Whilst reducing the present invention to practice, the present inventors have shown that sema3A, sema3D, sema3E and sema3G each function as potent anti-tumorigenic agents (FIGS. 2A-L; FIGS. 3A-I; FIGS. 4A-F). Specifically, injection of breast cancer cells expressing these semaphorins into nude mice resulted in tumors of reduced size as compared to tumors resulting from injection of tumor cells not expressing these semaphorins.

Whilst further reducing the present invention to practice, the present inventors have shown that semaphorin induced inhibition of tumor development from specific types of breast cancer cells is correlated with the expression of appropriate semaphorin receptors by the tumor cells. Although, the majority of the tested semaphorins also inhibited tumor angiogenesis, the present inventors showed that there was no correlation between inhibition of tumor angiogenesis and inhibition of tumor development. These results suggest that inhibition of tumor development by semaphorins depends on the expression of appropriate semaphorin receptors by tumor cells, and suggest that inhibition of angiogenesis is of lesser importance. They also suggest that tumors containing tumor cells expressing semaphorin receptors may be amenable to inhibition by appropriate sema3s and open the way for improved methods of personalized medicine for cancer treatment.

Thus, according to one aspect of the present invention, there is provided a method of selecting a semaphorin for treating cancer in a subject. The method comprises determining an expression of a semaphorin receptor on tumor cells of a tumor sample of the subject wherein an amount of the semaphorin receptor is indicative of the semaphorin suitable for treating the cancer in the subject.

As used herein, the term “semaphorin” refers to a mammalian polypeptide (e.g. human) belonging to the semaphorin family (including semaphorins of class 3, 4, 5, 6 and 7). Semaphorins typically function as signals during axon guidance and comprise a sema domain.

According to one embodiment, the semaphorin belongs to the class-3 semaphorin sub-family. Accordingly, the semaphorin may be semaphorin 3A (Genbank accession number NM_(—)006080, SEQ ID NO: 26); semaphorin 3B (Genbank accession number NM_(—)001005914, SEQ ID NO: 27); semaphorin 3C (Genbank accession number NM_(—)006379, SEQ ID NO: 28); semaphorin 3D (Genbank accession number NM_(—)152754, SEQ ID NO: 29); semaphorin 3E (Genbank accession number NM_(—)012431, SEQ ID NO: 30); semaphorin 3F (Genbank accession number NM_(—)004186, SEQ ID NO: 31); or semaphorin 3G (Genbank accession number NM_(—)020163, SEQ ID NO: 32).

A semaphorin of the present invention also refers to homologs (e.g., polypeptides which are at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 87%, at least 89%, at least 91%, at least 93%, at least 95% or more say 100% homologous to semaphorin sequences listed herein above as determined using BlastP software of the National Center of Biotechnology Information (NCBI) using default parameters). The homolog may also refer to a deletion, insertion, or substitution variant, including an amino acid substitution, thereof and biologically active polypeptide fragments thereof.

The term “treating” as used herein includes abrogating, substantially inhibiting, slowing or reversing the progression of the cancer, substantially ameliorating clinical or aesthetical symptoms of the cancer or substantially preventing the appearance of clinical or aesthetical symptoms of the cancer.

Typically, the subject for whom the semaphorin is selected is a mammalian subject e.g. a human.

As used herein the term “cancer” refers to the presence of cells possessing characteristics typical of cancer-causing cells, for example, uncontrolled proliferation, loss of specialized functions, immortality, significant metastatic potential, significant increase in anti-apoptotic activity, rapid growth and proliferation rate, and certain characteristic morphology and cellular markers. Typically, the cancer cells are in the form of a tumor; existing locally within an animal, or circulating in the blood stream as independent cells, for example, leukemic cells.

Specific examples of cancer for which semaphorins may be selected according to this aspect of the present invention include, but are not limited to, adrenocortical carcinoma, hereditary; bladder cancer; breast cancer; breast cancer, ductal; breast cancer, invasive intraductal; breast cancer, sporadic; breast cancer, susceptibility to; breast cancer, type 4; breast cancer, type 4; breast cancer-1; breast cancer-3; breast-ovarian cancer; Burkitt's lymphoma; cervical carcinoma; colorectal adenoma; colorectal cancer; colorectal cancer, hereditary nonpolyposis, type 1; colorectal cancer, hereditary nonpolyposis, type 2; colorectal cancer, hereditary nonpolyposis, type 3; colorectal cancer, hereditary nonpolyposis, type 6; colorectal cancer, hereditary nonpolyposis, type 7; dermatofibrosarcoma protuberans; endometrial carcinoma; esophageal cancer; gastric cancer, fibrosarcoma, glioblastoma multiforme; glomus tumors, multiple; hepatoblastoma; hepatocellular cancer; hepatocellular carcinoma; leukemia, acute lymphoblastic; leukemia, acute myeloid; leukemia, acute myeloid, with eosinophilia; leukemia, acute nonlymphocytic; leukemia, chronic myeloid; Li-Fraumeni syndrome; liposarcoma, lung cancer; lung cancer, small cell; lymphoma, non-Hodgkin's; lynch cancer family syndrome II; male germ cell tumor; mast cell leukemia; medullary thyroid; medulloblastoma; melanoma, meningioma; multiple endocrine neoplasia; myeloid malignancy, predisposition to; myxosarcoma, neuroblastoma; osteosarcoma; ovarian cancer; ovarian cancer, serous; ovarian carcinoma; ovarian sex cord tumors; pancreatic cancer; pancreatic endocrine tumors; paraganglioma, familial nonchromaffin; pilomatricoma; pituitary tumor, invasive; prostate adenocarcinoma; prostate cancer; renal cell carcinoma, papillary, familial and sporadic; retinoblastoma; rhabdoid predisposition syndrome, familial; rhabdoid tumors; rhabdomyosarcoma; small-cell cancer of lung; soft tissue sarcoma, squamous cell carcinoma, head and neck; T-cell acute lymphoblastic leukemia; Turcot syndrome with glioblastoma; tylosis with esophageal cancer; uterine cervix carcinoma, Wilms' tumor, type 2; and Wilms' tumor, type 1, and the like.

According to a particular embodiment of this aspect of the present invention, the cancer is breast cancer.

As mentioned, the method of the present invention is effected by determining an expression of a semaphorin receptor on tumor cells of a tumor sample of a subject.

As used herein, the phrase “semaphorin receptor” refers to a cell-surface polypeptide that is capable of binding to a semaphorin and transducing a response. Exemplary semaphorin receptors include, neuropilins, plexins and integrins.

Thus, for example, the neuropilin receptor may be a neuropilin 1 receptor (NP1; e.g. NM_(—)001024628; SEQ ID NO: 17) or a neuropilin 2 receptor (NP2; e.g. NM_(—)201279; SEQ ID NO: 18).

The plexin receptor may be a plexinA1 receptor (PlexA1; e.g. NM_(—)032242; SEQ ID NO: 19), a plexinA2 receptor (PlexA2; e.g. NM_(—)025179; SEQ ID NO: 20), a plexinA3 receptor (PlexA3; e.g. NM_(—)017514; SEQ ID NO: 21), a plexinA4 receptor (PlexA4; e.g. NM_(—)020911, SEQ ID NO: 22; NM_(—)001105543, SEQ ID NO: 23; NM_(—)181775, SEQ ID NO: 24) or a plexinD receptor (PlexD; e.g. NM_(—)015103, SEQ ID NO: 25).

Methods of determining an expression of a semaphorin receptor are known in the art. Specifically, determining an expression of semaphorin receptors may be effected on the RNA or protein level as detailed below.

Methods of Detecting Expression of a Semaphorin Receptor on the RNA Level

Northern Blot analysis: This method involves the detection of a particular RNA i.e. a semaphoring receptor RNA in a mixture of RNAs. An RNA sample is denatured by treatment with an agent (e.g., formaldehyde) that prevents hydrogen bonding between base pairs, ensuring that all the RNA molecules have an unfolded, linear conformation. The individual RNA molecules are then separated according to size by gel electrophoresis and transferred to a nitrocellulose or a nylon-based membrane to which the denatured RNAs adhere. The membrane is then exposed to labeled DNA probes. Probes may be labeled using radio-isotopes or enzyme linked nucleotides. Detection may be using autoradiography, colorimetric reaction or chemiluminescence. This method allows both quantitation of an amount of particular RNA molecules and determination of its identity by a relative position on the membrane which is indicative of a migration distance in the gel during electrophoresis.

RT-PCR analysis: This method uses PCR amplification of relatively rare RNAs molecules. First, RNA molecules are purified from the cells and converted into complementary DNA (cDNA) using a reverse transcriptase enzyme (such as an MMLV-RT) and primers such as, oligo dT, random hexamers or gene specific primers. Then by applying gene specific primers and Taq DNA polymerase, a PCR amplification reaction is carried out in a PCR machine. Those of skills in the art are capable of selecting the length and sequence of the gene specific primers and the PCR conditions (i.e., annealing temperatures, number of cycles and the like) which are suitable for detecting specific RNA molecules. It will be appreciated that a semi-quantitative RT-PCR reaction can be employed by adjusting the number of PCR cycles and comparing the amplification product to known controls. Exemplary primers that may be used to detect NRP1 receptors are set forth in SEQ ID NOs: 3 and 4. Exemplary primers that may be used to detect NRP2 receptors are set forth in SEQ ID NOs: 5 and 6. Exemplary primers that may be used to detect PLXNA1 receptors are set forth in SEQ ID NOs: 7 and 8. Exemplary primers that may be used to detect PLXNA2 receptors are set forth in SEQ ID NOs: 9 and 10. Exemplary primers that may be used to detect PLXNA3 receptors are set forth in SEQ ID NOs: 11 and 12. Exemplary primers that may be used to detect PLXNA4 receptors are set forth in SEQ ID NOs: 13 and 14. Exemplary primers that may be used to detect PLXND1 receptors are set forth in SEQ ID NOs: 15 and 16. Exemplary primers that may be used to detect CDH2 receptors are set forth in SEQ ID NOs: 1 and 2.

RNA in situ hybridization stain: In this method DNA or RNA probes are attached to the RNA molecules present in the cells. Generally, the cells are first fixed to microscopic slides to preserve the cellular structure and to prevent the RNA molecules from being degraded and then are subjected to hybridization buffer containing the labeled probe. The hybridization buffer includes reagents such as formamide and salts (e.g., sodium chloride and sodium citrate) which enable specific hybridization of the DNA or RNA probes with their target mRNA molecules in situ while avoiding non-specific binding of probe. Those of skills in the art are capable of adjusting the hybridization conditions (i.e., temperature, concentration of salts and formamide and the like) to specific probes and types of cells. Following hybridization, any unbound probe is washed off and the slide is subjected to either a photographic emulsion which reveals signals generated using radio-labeled probes or to a colorimetric reaction which reveals signals generated using enzyme-linked labeled probes.

In situ RT-PCR stain: This method is described in Nuovo G J, et al. [Intracellular localization of polymerase chain reaction (PCR)-amplified hepatitis C cDNA. Am J Surg Pathol. 1993, 17: 683-90] and Komminoth P, et al. [Evaluation of methods for hepatitis C virus detection in archival liver biopsies. Comparison of histology, immunohistochemistry, in situ hybridization, reverse transcriptase polymerase chain reaction (RT-PCR) and in situ RT-PCR. Pathol Res Pract. 1994, 190: 1017-25]. Briefly, the RT-PCR reaction is performed on fixed cells by incorporating labeled nucleotides to the PCR reaction. The reaction is carried on using a specific in situ RT-PCR apparatus such as the laser-capture microdissection PixCell I LCM system available from Arcturus Engineering (Mountainview, Calif.).

Oligonucleotide microarray—In this method oligonucleotide probes capable of specifically hybridizing with the polynucleotides encoding the semaphorin receptors of the present invention are attached to a solid surface (e.g., a glass wafer). Each oligonucleotide probe is of approximately 20-25 nucleic acids in length. To detect the expression pattern of the polynucleotides of the present invention in a specific cell sample (e.g., tumor cells), RNA is extracted from the cell sample using methods known in the art (using e.g., a TRIZOL solution, Gibco BRL, USA). Hybridization can take place using either labeled oligonucleotide probes (e.g., 5′-biotinylated probes) or labeled fragments of complementary DNA (cDNA) or RNA (cRNA). Briefly, double stranded cDNA is prepared from the RNA using reverse transcriptase (RT) (e.g., Superscript II RT), DNA ligase and DNA polymerase I, all according to manufacturer's instructions (Invitrogen Life Technologies, Frederick, Md., USA). To prepare labeled cRNA, the double stranded cDNA is subjected to an in vitro transcription reaction in the presence of biotinylated nucleotides using e.g., the BioArray High Yield RNA Transcript Labeling Kit (Enzo, Diagnostics, Affymetix Santa Clara Calif.). For efficient hybridization the labeled cRNA can be fragmented by incubating the RNA in 40 mM Tris Acetate (pH 8.1), 100 mM potassium acetate and 30 mM magnesium acetate for 35 minutes at 94° C. Following hybridization, the microarray is washed and the hybridization signal is scanned using a confocal laser fluorescence scanner which measures fluorescence intensity emitted by the labeled cRNA bound to the probe arrays.

For example, in the Affymetrix microarray (Affymetrix®, Santa Clara, Calif.) each gene on the array is represented by a series of different oligonucleotide probes, of which, each probe pair consists of a perfect match oligonucleotide and a mismatch oligonucleotide. While the perfect match probe has a sequence exactly complimentary to the particular gene, thus enabling the measurement of the level of expression of the particular gene, the mismatch probe differs from the perfect match probe by a single base substitution at the center base position. The hybridization signal is scanned using the Agilent scanner, and the Microarray Suite software subtracts the non-specific signal resulting from the mismatch probe from the signal resulting from the perfect match probe.

Methods of Detecting Semaphorin Receptors on the Protein Level

Determining expression of a semaphorin receptor on the protein level is typically effected using an antibody capable of specifically binding with a particular semaphorin receptor.

Exemplary antibodies capable of specifically interacting with NP1 and NP2 are widely available e.g. from Santa-Cruz Biotechnology (Santa Cruz, Calif., Catalogue nos. sc-12122, sc 12123, sc-12125, sc-12128 and sc-50408).

Exemplary antibodies capable of specifically interacting with plexin receptors are also widely available e.g. from Santa-Cruz Biotechnology (Santa Cruz, Calif., Catalogue Nos. sc-25639, sc-10138, sc-10139, sc-10144, sc-25640, sc-10143, sc-25641, sc-10135, sc-10134, sc-28372, sc10147, sc-25642, sc-10145, sc-67034, sc-34504, sc-34506, sc-34507, sc-46240, sc-67144, sc-46241, sc-46242, sc46243, sc-10152, sc-10149, sc-46244, sc-46245, sc-67145, sc-46246 and sc-46247. Antibodies are also available from Abcam Mass., U.S.A. (Catalogue Nos. ab32960, ab23391, ab39350, ab39357, ab39008, ab41564 and ab39715).

Preferably, the antibody specifically binds at least one epitope of the semaphorin receptor. As used herein, the term “epitope” refers to any antigenic determinant on an antigen to which the paratope of an antibody binds.

Epitopic determinants usually consist of chemically active surface groupings of molecules such as amino acids or carbohydrate side chains and usually have specific three dimensional structural characteristics, as well as specific charge characteristics.

The term “antibody” as used in this invention includes intact molecules as well as functional fragments thereof, such as Fab, F(ab′)2, and Fv that are capable of binding to macrophages. These functional antibody fragments are defined as follows: (1) Fab, the fragment which contains a monovalent antigen-binding fragment of an antibody molecule, can be produced by digestion of whole antibody with the enzyme papain to yield an intact light chain and a portion of one heavy chain; (2) Fab′, the fragment of an antibody molecule that can be obtained by treating whole antibody with pepsin, followed by reduction, to yield an intact light chain and a portion of the heavy chain; two Fab′ fragments are obtained per antibody molecule; (3) (Fab′)2, the fragment of the antibody that can be obtained by treating whole antibody with the enzyme pepsin without subsequent reduction; F(ab′)2 is a dimer of two Fab′ fragments held together by two disulfide bonds; (4) Fv, defined as a genetically engineered fragment containing the variable region of the light chain and the variable region of the heavy chain expressed as two chains; and (5) Single chain antibody (“SCA”), a genetically engineered molecule containing the variable region of the light chain and the variable region of the heavy chain, linked by a suitable polypeptide linker as a genetically fused single chain molecule.

Methods of producing polyclonal and monoclonal antibodies as well as fragments thereof which bind to specific semaphorin receptors are well known in the art (See for example, Harlow and Lane, Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory, New York, 1988, incorporated herein by reference).

Methods of detecting semaphorin receptors include immunoassays which include but are not limited to competitive and non-competitive assay systems using techniques such as Western blots, radioimmunoassays, ELISA (enzyme linked immunosorbent assay), “sandwich” immunoassays, and immunoprecipitation assays and immunohistochemical assays as detailed herein below.

Enzyme linked immunosorbent assay (ELISA): This method involves fixation of a sample (e.g., fixed cells or a proteinaceous solution) containing a protein substrate to a surface such as a well of a microtiter plate. A substrate specific antibody coupled to an enzyme is applied and allowed to bind to the substrate. Presence of the antibody is then detected and quantitated by a colorimetric reaction employing the enzyme coupled to the antibody. Enzymes commonly employed in this method include horseradish peroxidase and alkaline phosphatase. If well calibrated and within the linear range of response, the amount of substrate present in the sample is proportional to the amount of color produced. A substrate standard is generally employed to improve quantitative accuracy.

Western blot: This method involves separation of a substrate from other protein by means of an acrylamide gel followed by transfer of the substrate to a membrane (e.g., nylon or PVDF). Presence of the substrate is then detected by antibodies specific to the substrate, which are in turn detected by antibody binding reagents. Antibody binding reagents may be, for example, protein A, or other antibodies. Antibody binding reagents may be radiolabeled or enzyme linked as described hereinabove. Detection may be by autoradiography, colorimetric reaction or chemiluminescence. This method allows both quantitation of an amount of substrate and determination of its identity by a relative position on the membrane which is indicative of a migration distance in the acrylamide gel during electrophoresis.

Radio-immunoassay (RIA): In one version, this method involves precipitation of the desired protein (i.e., the substrate) with a specific antibody and radiolabeled antibody binding protein (e.g., protein A labeled with I¹²⁵) immobilized on a precipitable carrier such as agarose beads. The number of counts in the precipitated pellet is proportional to the amount of substrate.

In an alternate version of the RIA, a labeled substrate and an unlabelled antibody binding protein are employed. A sample containing an unknown amount of substrate is added in varying amounts. The decrease in precipitated counts from the labeled substrate is proportional to the amount of substrate in the added sample.

Fluorescence activated cell sorting (FACS): This method involves detection of a substrate in situ in cells by substrate specific antibodies. The substrate specific antibodies are linked to fluorophores. Detection is by means of a cell sorting machine which reads the wavelength of light emitted from each cell as it passes through a light beam. This method may employ two or more antibodies simultaneously.

Immunohistochemical analysis: This method involves detection of a substrate in situ in fixed cells by substrate specific antibodies. The substrate specific antibodies may be enzyme linked or linked to fluorophores. Detection is by microscopy and subjective or automatic evaluation. If enzyme linked antibodies are employed, a colorimetric reaction may be required. It will be appreciated that immunohistochemistry is often followed by counterstaining of the cell nuclei using for example Hematoxyline or Giemsa stain.

In situ activity assay: According to this method, a chromogenic substrate is applied on the cells containing an active enzyme and the enzyme catalyzes a reaction in which the substrate is decomposed to produce a chromogenic product visible by a light or a fluorescent microscope.

It will be appreciated that the tumor cells of the subject are obtained from a tumor sample e.g. during a tumor biopsy.

As mentioned, the amount of the semaphorin receptor is indicative of the semaphorin suitable for treating the cancer in the subject.

It will be appreciated that the amount of the semaphorin receptor should be sufficient to transduce a biological response (i.e. tumor inhibition). The amount of receptor sufficient to generate such a response is typically dependent on the affinity of the semaphorin for that receptor. Thus, for example if a semaphorin has a high affinity for a receptor (e.g. comprises a Km of about 10⁻⁷ M, 10⁻⁸ M, 10⁻⁹ M, 10⁻¹⁰ M or even 10⁻¹¹M), the amount of receptor does not have to be as great the amount of receptor for which the semaphorin has a low affinity receptor (e.g. comprises a Km of about 10⁻⁶ M 10⁻⁵M, 10⁻⁴ M, 10⁻³ M).

According to one embodiment, the amount of receptor on the tumor cells is at least 20% the total number of semaphorin receptors on the tumor cells. According to another embodiment, the amount of receptor on the tumor cells is at least 30% the total number of semaphorin receptors on the tumor cells. According to another embodiment, the amount of receptor on the tumor cells is at least 40% the total number of semaphorin receptors on the tumor cells. According to another embodiment, the amount of receptor on the tumor cells is at least 50% the total number of semaphorin receptors on the tumor cells. According to another embodiment, the amount of receptor on the tumor cells is at least 60% the total number of semaphorin receptors on the tumor cells. According to another embodiment, the amount of receptor on the tumor cells is at least 70% the total number of semaphorin receptors on the tumor cells. According to another embodiment, the amount of receptor on the tumor cells is at least 80% the total number of semaphorin receptors on the tumor cells.

Accordingly, the present inventors have found that if a sufficient quantity of NP1 receptors are located on the tumor cells, the most preferable semaphorin for treatment comprises Sema3A or Sema3D. If a sufficient quantity of NP2 receptors are located on the tumor cells, the most preferable semaphorin for treatment comprises Sema3G or Sema3F. If a sufficient quantity of PlexD1 receptors are located on the tumor cells, the most preferable semaphorin for treatment comprises Sema3E.

It will be appreciated that selection of the semaphorin is not only based on the quantity of a receptor, but also expression profile of a plurality of semaphorin receptors subtypes. For example, it is known that neuropilins form spontaneous complexes with several members of the plexin receptor family. Accordingly, selection of the semaphorin may also be effected based on the expression pattern of both the neuropilin receptor and the plexin receptor.

The present inventors have also found that an additional method for selecting a semaphorin for treating a cancer. Semaphorins that were shown to inhibit the anchorage independent growth of a particular tumor cell were also shown to be effective at inhibiting tumor formation. A method of measuring anchorage independent growth of tumor cells is described in the Materials and Methods section of the Examples herein below involving measurement of colonies in soft agar.

It will be appreciated that the agents used for detecting semaphorin receptor expression may be provided as a kit, such as an FDA-approved kit, which may contain one or more unit dosage form containing the active agent (e.g. antibody or probe capable of specifically interacting with a semaphorin subtype). The kit may also comprise other agents useful for analyzing semaphorin receptor expression (e.g. suitable buffers, control antibodies or probes). In addition, the kit may comprise agents used for measuring tumor colonies in soft agar.

The kit may be accompanied by instructions for administration. The kit may also be accompanied by a notice in a form prescribed by a governmental agency regulating the manufacture, use, or sale of pharmaceuticals, which notice is reflective of approval by the agency of the form of the compositions for human or veterinary administration. Such notice, for example, may include labeling approved by the U.S. Food and Drug Administration.

Following selection, treatment of the cancer may be initiated by contacting (either in vivo or ex vivo) the cancer cells with an agent capable of upregulating the appropriate semaphorin.

Accordingly, the present invention contemplates administration of therapeutically effective amounts of semaphorins themselves, or administration of polynucleotides encoding the semaphorins (i.e. gene therapy) to subjects in need thereof in order to treat cancer.

The semaphorins polypeptides may comprise the full length sequences of those set forth in SEQ ID NOs: 26-32. Alternatively the semaphorins may be homologs (e.g., polypeptides which are at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 87%, at least 89%, at least 91%, at least 93%, at least 95% or more say 100% homologous to semaphorin sequences listed herein above as determined using BlastP software of the National Center of Biotechnology Information (NCBI) using default parameters) comprising semaphorin activity. The homolog may also refer to a deletion, insertion, or substitution variant, including an amino acid substitution, thereof and biologically active polypeptide fragments thereof.

The term “polypeptide” as used herein refers to a polymer of natural or synthetic amino acids, encompassing native peptides (either degradation products, synthetically synthesized polypeptides or recombinant polypeptides) and peptidomimetics (typically, synthetically synthesized peptides), as well as peptoids and semipeptoids which are polypeptide analogs, which may have, for example, modifications rendering the peptides even more stable while in a body or more capable of penetrating into cells.

Such modifications include, but are not limited to N terminus modification, C terminus modification, polypeptide bond modification, including, but not limited to, CH₂—NH, CH₂—S, CH₂—S═O, O═C—NH, CH₂—O, CH₂—CH₂, S═C—NH, CH═CH or CF═CH, backbone modifications, and residue modification. Methods for preparing peptidomimetic compounds are well known in the art and are specified, for example, in Quantitative Drug Design, C. A. Ramsden Gd., Chapter 17.2, F. Choplin Pergamon Press (1992), which is incorporated by reference as if fully set forth herein. Further details in this respect are provided hereinunder.

Polypeptide bonds (—CO—NH—) within the polypeptide may be substituted, for example, by N-methylated bonds (—N(CH3)-CO—), ester bonds (—C(R)H—C—O—O—C(R)—N—), ketomethylen bonds (—CO—CH2-), α-aza bonds (—NH—N(R)—CO—), wherein R is any alkyl, e.g., methyl, carba bonds (—CH2-NH—), hydroxyethylene bonds (—CH(OH)—CH2-), thioamide bonds (—CS—NH—), olefinic double bonds (—CH═CH—), retro amide bonds (—NH—CO—), polypeptide derivatives (—N(R)—CH2-CO—), wherein R is the “normal” side chain, naturally presented on the carbon atom.

These modifications can occur at any of the bonds along the polypeptide chain and even at several (2-3) at the same time.

Natural aromatic amino acids, Trp, Tyr and Phe, may be substituted for synthetic non-natural acid such as Phenylglycine, TIC, naphthylelanine (Nol), ring-methylated derivatives of Phe, halogenated derivatives of Phe or o-methyl-Tyr.

In addition to the above, the polypeptides of the present invention may also include one or more modified amino acids or one or more non-amino acid monomers (e.g. fatty acids, complex carbohydrates etc).

As used herein in the specification and in the claims section below the term “amino acid” or “amino acids” is understood to include the 20 naturally occurring amino acids; those amino acids often modified post-translationally in vivo, including, for example, hydroxyproline, phosphoserine and phosphothreonine; and other unusual amino acids including, but not limited to, 2-aminoadipic acid, hydroxylysine, isodesmosine, nor-valine, nor-leucine and ornithine. Furthermore, the term “amino acid” includes both D- and L-amino acids (stereoisomers).

Tables 1 and 2 below list naturally occurring amino acids (Table 1) and non-conventional or modified amino acids (Table 2) which can be used with the present invention.

TABLE 1 Three-Letter Amino Acid Abbreviation One-letter Symbol alanine Ala A Arginine Arg R Asparagine Asn N Aspartic acid Asp D Cysteine Cys C Glutamine Gln Q Glutamic Acid Glu E glycine Gly G Histidine His H isoleucine Iie I leucine Leu L Lysine Lys K Methionine Met M phenylalanine Phe F Proline Pro P Serine Ser S Threonine Thr T tryptophan Trp W tyrosine Tyr Y Valine Val V Any amino acid as above Xaa X

TABLE 2 Non-conventional Non-conventional amino acid Code amino acid Code α-aminobutyric acid Abu L-N-methylalanine Nmala α-amino-α-methylbutyrate Mgabu L-N-methylarginine Nmarg aminocyclopropane- Cpro L-N-methylasparagine Nmasn carboxylate L-N-methylaspartic acid Nmasp aminoisobutyric acid Aib L-N-methylcysteine Nmcys aminonorbornyl-carboxylate Norb L-N-methylglutamine Nmgin L-N-methylglutamic Nmglu acid cyclohexylalanine Chexa L-N-methylhistidine Nmhis cyclopentylalanine Cpen L-N-methylisolleucine Nmile D-alanine Dal L-N-methylleucine Nmleu D-arginine Darg L-N-methyllysine Nmlys D-aspartic acid Dasp L-N-methylmethionine Nmmet D-cysteine Dcys L-N-methylnorleucine Nmnle D-glutamine Dgln L-N-methylnorvaline Nmnva D-glutamic acid Dglu L-N-methylornithine Nmorn D-histidine Dhis L-N- Nmphe methylphenylalanine D-isoleucine Dile L-N-methylproline Nmpro D-leucine Dleu L-N-methylserine Nmser D-lysine Dlys L-N-methylthreonine Nmthr D-methionine Dmet L-N-methyltryptophan Nmtrp D-ornithine Dorn L-N-methyltyrosine Nmtyr D-phenylalanine Dphe L-N-methylvaline Nmval D-proline Dpro L-N-methylethylglycine Nmetg D-serine Dser L-N-methyl-t- Nmtbug butylglycine D-threonine Dthr L-norleucine Nle D-tryptophan Dtrp L-norvaline Nva D-tyrosine Dtyr α-methyl- Maib aminoisobutyrate D-valine Dval α-methyl-γ- Mgabu aminobutyrate D-α-methylalanine Dmala α-methylcyclohexylalanine Mchexa D-α-methylarginine Dmarg α- Mcpen methylcyclopentylalanine D-α-methylasparagine Dmasn α-methyl-α- Manap napthylalanine D-α-methylaspartate Dmasp α-methylpenicillamine Mpen D-α-methylcysteine Dmcys N-(4-aminobutyl)glycine Nglu D-α-methylglutamine Dmgln N-(2-aminoethyl)glycine Naeg D-α-methylhistidine Dmhis N-(3- Norn aminopropyl)glycine D-α-methylisoleucine Dmile N-amino-α- Nmaabu methylbutyrate D-α-methylleucine Dmleu α-napthylalanine Anap D-α-methyllysine Dmlys N-benzylglycine Nphe D-α-methylmethionine Dmmet N-(2- Ngln carbamylethyl)glycine D-α-methylornithine Dmorn N- Nasn (carbamylmethyl)glycine D-α-methylphenylalanine Dmphe N-(2- Nglu carboxyethyl)glycine D-α-methylproline Dmpro N- Nasp (carboxymethyl)glycine D-α-methylserine Dmser N-cyclobutylglycine Ncbut D-α-methylthreonine Dmthr N-cycloheptylglycine Nchep D-α-methyltryptophan Dmtrp N-cyclohexylglycine Nchex D-α-methyltyrosine Dmty N-cyclodecylglycine Ncdec D-α-methylvaline Dmval N-cyclododeclglycine Ncdod D-α-methylalnine Dnmala N-cyclooctylglycine Ncoct D-α-methylarginine Dnmarg N-cyclopropylglycine Ncpro D-α-methylasparagine Dnmasn N-cycloundecylglycine Ncund D-α-methylasparatate Dnmasp N-(2,2- Nbhm diphenylethyl)glycine D-α-methylcysteine Dnmcys N-(3,3- Nbhe diphenylpropyl)glycine D-N-methylleucine Dnmleu N-(3-indolylyethyl)glycine Nhtrp D-N-methyllysine Dnmlys N-methyl-γ- Nmgabu aminobutyrate N-methylcyclohexylalanine Nmchex D-N-methylmethionine Dnmmet D-N-methylornithine Dnmorn N- Nmcpen methylcyclopentylalanine N-methylglycine Nala D-N- Dnmphe methylphenylalanine N-methylaminoisobutyrate Nmaib D-N-methylproline Dnmpro N-(1-methylpropyl)glycine Nile D-N-methylserine Dnmser N-(2-methylpropyl)glycine Nile D-N-methylserine Dnmser N-(2-methylpropyl)glycine Nleu D-N-methylthreonine Dnmthr D-N-methyltryptophan Dnmtrp N-(1- Nva methylethyl)glycine D-N-methyltyrosine Dnmtyr N-methylanapthylalanine Nmanap D-N-methylvaline Dnmval N-methylpenicillamine Nmpen γ-aminobutyric acid Gabu N-(p- Nhtyr hydroxyphenyl)glycine L-t-butylglycine Tbug N-(thiomethyl)glycine Ncys L-ethylglycine Etg penicillamine Pen L-homophenylalanine Hphe L-α-methylalanine Mala L-α-methylarginine Marg L-α-methylasparagine Masn L-α-methylaspartate Masp L-α-methyl-t- Mtbug butylglycine L-α-methylcysteine Mcys L-methylethylglycine Metg L-α-methylglutamine Mgln L-α-methylglutamate Mglu L-α-methylhistidine Mhis L-α-methylhomophenylalanine Mhphe L-α-methylisoleucine Mile N-(2- Nmet methylthioethyl)glycine D-N-methylglutamine Dnmgln N-(3- Narg guanidinopropyl)glycine D-N-methylglutamate Dnmglu N-(1- Nthr hydroxyethyl)glycine D-N-methylhistidine Dnmhis N-(hydroxyethyl)glycine Nser D-N-methylisoleucine Dnmile N- Nhis (imidazolylethyl)glycine D-N-methylleucine Dnmleu N-(3- Nhtrp indolylyethyl)glycine D-N-methyllysine Dnmlys N-methyl-γ- Nmgabu aminobutyrate N-methylcyclohexylalanine Nmchex D-N-methylmethionine Dnmmet D-N-methylornithine Dnmorn N- Nmcpen methylcyclopentylalanine N-methylglycine Nala D-N- Dnmphe methylphenylalanine N-methylaminoisobutyrate Nmaib D-N-methylproline Dnmpro N-(1-methylpropyl)glycine Nile D-N-methylserine Dnmser N-(2-methylpropyl)glycine Nleu D-N-methylthreonine Dnmthr D-N-methyltryptophan Dnmtrp N-(1- Nval methylethyl)glycine D-N-methyltyrosine Dnmtyr N-methyla- Nmanap napthylalanine D-N-methylvaline Dnmval N-methylpenicillamine Nmpen γ-aminobutyric acid Gabu N-(p- Nhtyr hydroxyphenyl)glycine L-t-butylglycine Tbug N-(thiomethyl)glycine Ncys L-ethylglycine Etg penicillamine Pen L-homophenylalanine Hphe L-α-methylalanine Mala L-α-methylarginine Marg L-α-methylasparagine Masn L-α-methylaspartate Masp L-α-methyl-t- Mtbug butylglycine L-α-methylcysteine Mcys L-methylethylglycine Metg L-α-methylglutamine Mgln L-α-methylglutamate Mglu L-α ethylhistidine Mhis L-α- Mhphe methylhomophenylalanine L-α thylisoleucine Mile N-(2- Nmet methylthioethyl)glycine L-α-methylleucine Mleu L-α-methyllysine Mlys L-α-methylmethionine Mmet L-α-methylnorleucine Mnle L-α-methylnorvaline Mnva L-α-methylornithine Morn L-α-methylphenylalanine Mphe L-α-methylproline Mpro L-α-methylserine mser L-α-methylthreonine Mthr L-α ethylvaline Mtrp L-α-methyltyrosine Mtyr L-α-methylleucine Mval L-N-methylhomophenylalanine Nmhphe nbhm N-(N-(2,2-diphenylethyl) N-(N-(3,3- diphenylpropyl) carbamylmethyl-glycine Nnbhm carbamylmethyl(1)glycine Nnbhe 1-carboxy-1-(2,2- Nmbc diphenyl hylamino)cyclopropane

Table 2 Cont.

As mentioned herein above, the semaphorin of the present invention may comprise a conservative or non-conservative substitution.

The term “conservative substitution” as used herein, refers to the replacement of an amino acid present in the native sequence in the peptide with a naturally or non-naturally occurring amino or a peptidomimetics having similar steric properties. Where the side-chain of the native amino acid to be replaced is either polar or hydrophobic, the conservative substitution should be with a naturally occurring amino acid, a non-naturally occurring amino acid or with a peptidomimetic moiety which is also polar or hydrophobic (in addition to having the same steric properties as the side-chain of the replaced amino acid).

As naturally occurring amino acids are typically grouped according to their properties, conservative substitutions by naturally occurring amino acids can be easily determined bearing in mind the fact that in accordance with the invention replacement of charged amino acids by sterically similar non-charged amino acids are considered as conservative substitutions.

For producing conservative substitutions by non-naturally occurring amino acids it is also possible to use amino acid analogs (synthetic amino acids) well known in the art. A peptidomimetic of the naturally occurring amino acid is well documented in the literature known to the skilled practitioner.

When affecting conservative substitutions the substituting amino acid should have the same or a similar functional group in the side chain as the original amino acid.

The phrase “non-conservative substitutions” as used herein refers to replacement of the amino acid as present in the parent sequence by another naturally or non-naturally occurring amino acid, having different electrochemical and/or steric properties. Thus, the side chain of the substituting amino acid can be significantly larger (or smaller) than the side chain of the native amino acid being substituted and/or can have functional groups with significantly different electronic properties than the amino acid being substituted. Examples of non-conservative substitutions of this type include the substitution of phenylalanine or cyclohexylmethyl glycine for alanine, isoleucine for glycine, or —NH—CH[(—CH₂)₅—COOH]—CO— for aspartic acid. Those non-conservative substitutions which fall under the scope of the present invention are those which still constitute a peptide having semaphorin-like properties.

As mentioned, the semaphorins of the present invention may comprise substitutions. According to one embodiment, the semaphorin may be engineered to resist cleavage by furin-like pro-protein convertases. Thus, for example the pro-protein convertase recognition sequence RFRR (SEQ ID NO: 39) may be mutated into the sequence KFKK (SEQ ID NO: 40). This has been effected for semaphorin-3B, where the authors showed that this mutation conferred partial resistance to pro-protein convertases of cancer cells without affecting the biological activity of full length semaphorin-3B [Varshaysky A, Kessler O, Abramovitch S, Kigel B, Zaffryar S, et al (2008) Cancer Res 68:6922-6931]. Exemplary polypeptide and polynucleotide sequences of semaphorins that are at least partially resistant to pro-protein convertase are set forth in SEQ ID NOs: 33-38.

As mentioned, the N and C termini of the peptides of the present invention may be protected by functional groups. Suitable functional groups are described in Green and Wuts, “Protecting Groups in Organic Synthesis”, John Wiley and Sons, Chapters 5 and 7, 1991, the teachings of which are incorporated herein by reference. Preferred protecting groups are those that facilitate transport of the compound attached thereto into a cell, for example, by reducing the hydrophilicity and increasing the lipophilicity of the compounds.

These moieties can be cleaved in vivo, either by hydrolysis or enzymatically, inside the cell. Hydroxyl protecting groups include esters, carbonates and carbamate protecting groups. Amine protecting groups include alkoxy and aryloxy carbonyl groups, as described above for N-terminal protecting groups. Carboxylic acid protecting groups include aliphatic, benzylic and aryl esters, as described above for C-terminal protecting groups. In one embodiment, the carboxylic acid group in the side chain of one or more glutamic acid or aspartic acid residue in a peptide of the present invention is protected, preferably with a methyl, ethyl, benzyl or substituted benzyl ester.

Examples of N-terminal protecting groups include acyl groups (—CO—R1) and alkoxy carbonyl or aryloxy carbonyl groups (—CO—O—R1), wherein R1 is an aliphatic, substituted aliphatic, benzyl, substituted benzyl, aromatic or a substituted aromatic group. Specific examples of acyl groups include acetyl, (ethyl)-CO—, n-propyl-CO—, iso-propyl-CO—, n-butyl-CO—, sec-butyl-CO—, t-butyl-CO—, hexyl, lauroyl, palmitoyl, myristoyl, stearyl, oleoyl phenyl-CO—, substituted phenyl-CO—, benzyl-CO— and (substituted benzyl)-CO—. Examples of alkoxy carbonyl and aryloxy carbonyl groups include CH3-O—CO—, (ethyl)-O—CO—, n-propyl-O—CO—, iso-propyl-O—CO—, n-butyl-O—CO—, sec-butyl-O—CO—, t-butyl-O—CO—, phenyl-O—CO—, substituted phenyl-O—CO— and benzyl-O—CO—, (substituted benzyl)-O—CO—. Adamantan, naphtalen, myristoleyl, tuluen, biphenyl, cinnamoyl, nitrobenzoy, toluoyl, furoyl, benzoyl, cyclohexane, norbornane, Z-caproic. In order to facilitate the N-acylation, one to four glycine residues can be present in the N-terminus of the molecule.

The carboxyl group at the C-terminus of the compound can be protected, for example, by an amide (i.e., the hydroxyl group at the C-terminus is replaced with —NH₂, —NHR₂ and —NR₂R₃) or ester (i.e. the hydroxyl group at the C-terminus is replaced with —OR₂). R₂ and R₃ are independently an aliphatic, substituted aliphatic, benzyl, substituted benzyl, aryl or a substituted aryl group. In addition, taken together with the nitrogen atom, R₂ and R₃ can form a C4 to C8 heterocyclic ring with from about 0-2 additional heteroatoms such as nitrogen, oxygen or sulfur. Examples of suitable heterocyclic rings include piperidinyl, pyrrolidinyl, morpholino, thiomorpholino or piperazinyl. Examples of C-terminal protecting groups include —NH₂, —NHCH₃, —N(CH₃)₂, —NH(ethyl), —N(ethyl)₂, —N(methyl) (ethyl), —NH(benzyl), —N(C1-C4 alkyl)(benzyl), —NH(phenyl), —N(C1-C4 alkyl) (phenyl), —OCH₃, —O-(ethyl), —O-(n-propyl), —O-(n-butyl), —O-(iso-propyl), —O-(sec-butyl), —O-(t-butyl), —O-benzyl and —O-phenyl.

The sempahorins of the present invention may also comprise non-amino acid moieties, such as for example, hydrophobic moieties (various linear, branched, cyclic, polycyclic or hetrocyclic hydrocarbons and hydrocarbon derivatives) attached to the peptides; various protecting groups, especially where the compound is linear, which are attached to the compound's terminals to decrease degradation. Chemical (non-amino acid) groups present in the compound may be included in order to improve various physiological properties such; decreased degradation or clearance; decreased repulsion by various cellular pumps, improve immunogenic activities, improve various modes of administration (such as attachment of various sequences which allow penetration through various barriers, through the gut, etc.); increased specificity, increased affinity, decreased toxicity and the like.

According to one embodiment, the sempahorins of the present invention are attached to a sustained-release enhancing agent. Exemplary sustained-release enhancing agents include, but are not limited to hyaluronic acid (HA), alginic acid (AA), polyhydroxyethyl methacrylate (Poly-HEMA), polyethylene glycol (PEG), glyme and polyisopropylacrylamide.

Attaching the amino acid sequence component of the semaphorins of the invention to other non-amino acid agents may be by covalent linking, by non-covalent complexion, for example, by complexion to a hydrophobic polymer, which can be degraded or cleaved producing a compound capable of sustained release; by entrapping the amino acid part of the semaphorin in liposomes or micelles to produce the final semaphorin of the invention. The association may be by the entrapment of the amino acid sequence within the other component (liposome, micelle) or the impregnation of the amino acid sequence within a polymer to produce the final peptide of the invention.

The semaphorins of the present invention can be biochemically synthesized such as by using standard solid phase techniques. These methods include exclusive solid phase synthesis, partial solid phase synthesis methods, fragment condensation, classical solution synthesis. Solid phase peptide synthesis procedures are well known in the art and further described by John Morrow Stewart and Janis Dillaha Young, Solid Phase Polypeptide Syntheses (2nd Ed., Pierce Chemical Company, 1984).

Recombinant techniques may also be used to generate the semaphorins of the present invention. These techniques may be preferred due to the number of amino acids in a semaphorin polypeptide and the large amounts required thereof. Such recombinant techniques are described by Bitter et al., (1987) Methods in Enzymol. 153:516-544, Studier et al. (1990) Methods in Enzymol. 185:60-89, Brisson et al. (1984) Nature 310:511-514, Takamatsu et al. (1987) EMBO J. 6:307-311, Coruzzi et al. (1984) EMBO J. 3:1671-1680 and Brogli et al., (1984) Science 224:838-843, Gurley et al. (1986) Mol. Cell. Biol. 6:559-565 and Weissbach & Weissbach, 1988, Methods for Plant Molecular Biology, Academic Press, NY, Section VIII, pp 421-463.

To produce an expression vector for the expression of the semaphorins of the present invention, a polynucleotide encoding the semaphorins of the present invention are ligated into a nucleic acid expression vector, which comprises the polynucleotide sequence under the transcriptional control of a cis-regulatory sequence (e.g., promoter sequence) suitable for directing constitutive, tissue specific or inducible transcription of the semaphorins of the present invention in the host cells.

The phrase “an isolated polynucleotide” refers to a single or double stranded nucleic acid sequence which is isolated and provided in the form of an RNA sequence, a complementary polynucleotide sequence (cDNA), a genomic polynucleotide sequence and/or a composite polynucleotide sequences (e.g., a combination of the above).

As used herein the phrase “complementary polynucleotide sequence” refers to a sequence, which results from reverse transcription of messenger RNA using a reverse transcriptase or any other RNA dependent DNA polymerase. Such a sequence can be subsequently amplified in vivo or in vitro using a DNA dependent DNA polymerase.

As used herein the phrase “genomic polynucleotide sequence” refers to a sequence derived (isolated) from a chromosome and thus it represents a contiguous portion of a chromosome.

As used herein the phrase “composite polynucleotide sequence” refers to a sequence, which is at least partially complementary and at least partially genomic. A composite sequence can include some exonal sequences required to encode the semaphorin of the present invention, as well as some intronic sequences interposing therebetween. The intronic sequences can be of any source, including of other genes, and typically will include conserved splicing signal sequences. Such intronic sequences may further include cis acting expression regulatory elements.

As mentioned hereinabove, polynucleotide sequences of the present invention are inserted into expression vectors (i.e., a nucleic acid construct) to enable expression of the recombinant semaphorin. The expression vector of the present invention may include additional sequences which render this vector suitable for replication and integration in prokaryotes, eukaryotes, or preferably both (e.g., shuttle vectors). Typical cloning vectors contain transcription and translation initiation sequences (e.g., promoters, enhances) and transcription and translation terminators (e.g., polyadenylation signals).

A variety of prokaryotic or eukaryotic cells can be used as host-expression systems to express the semaphorins of the present invention. These include, but are not limited to, microorganisms, such as bacteria transformed with a recombinant bacteriophage DNA, plasmid DNA or cosmid DNA expression vector containing the semaphorin coding sequence; yeast transformed with recombinant yeast expression vectors containing the semaphorin coding sequence; plant cell systems infected with recombinant virus expression vectors (e.g., cauliflower mosaic virus, CaMV; tobacco mosaic virus, TMV) or transformed with recombinant plasmid expression vectors, such as Ti plasmid, containing the semaphorin coding sequence.

Other than containing the necessary elements for the transcription and translation of the inserted coding sequence (encoding the semaphorin), the expression construct of the present invention can also include sequences engineered to optimize stability, production, purification, yield or activity of the expressed semaphorin.

Various methods can be used to introduce the expression vector of the present invention into the host cell system. Such methods are generally described in Sambrook et al., Molecular Cloning: A Laboratory Manual, Cold Springs Harbor Laboratory, New York (1989, 1992), in Ausubel et al., Current Protocols in Molecular Biology, John Wiley and Sons, Baltimore, Md. (1989), Chang et al., Somatic Gene Therapy, CRC Press, Ann Arbor, Mich. (1995), Vega et al., Gene Targeting, CRC Press, Ann Arbor Mich. (1995), Vectors: A Survey of Molecular Cloning Vectors and Their Uses, Butterworths, Boston Mass. (1988) and Gilboa et al. [Biotechniques 4 (6): 504-512, 1986] and include, for example, stable or transient transfection, lipofection, electroporation and infection with recombinant viral vectors. In addition, see U.S. Pat. Nos. 5,464,764 and 5,487,992 for positive-negative selection methods.

Transformed cells are cultured under effective conditions, which allow for the expression of high amounts of recombinant peptide. Effective culture conditions include, but are not limited to, effective media, bioreactor, temperature, pH and oxygen conditions that permit protein production. An effective medium refers to any medium in which a cell is cultured to produce the recombinant semaphorin of the present invention. Such a medium typically includes an aqueous solution having assimilable carbon, nitrogen and phosphate sources, and appropriate salts, minerals, metals and other nutrients, such as vitamins. Cells of the present invention can be cultured in conventional fermentation bioreactors, shake flasks, test tubes, microtiter dishes and petri plates. Culturing can be carried out at a temperature, pH and oxygen content appropriate for a recombinant cell. Such culturing conditions are within the expertise of one of ordinary skill in the art.

Depending on the vector and host system used for production, resultant semaphorins of the present invention may either remain within the recombinant cell, secreted into the fermentation medium, secreted into a space between two cellular membranes, such as the periplasmic space in E. coli; or retained on the outer surface of a cell or viral membrane.

Following a predetermined time in culture, recovery of the recombinant semaphorin is effected.

The phrase “recovering the recombinant semaphorin” used herein refers to collecting the whole fermentation medium containing the semaphorin and need not imply additional steps of separation or purification.

Thus, the semaphorins of the present invention can be purified using a variety of standard protein purification techniques, such as, but not limited to, affinity chromatography, ion exchange chromatography, filtration, electrophoresis, hydrophobic interaction chromatography, gel filtration chromatography, reverse phase chromatography, concanavalin A chromatography, chromatofocusing and differential solubilization.

To facilitate recovery, the expressed coding sequence can be engineered to encode a semaphorin fused to a cleavable moiety. Such a fusion protein can be designed so that the semaphorin can be readily isolated by affinity chromatography; e.g., by immobilization on a column specific for the cleavable moiety. Where a cleavage site is engineered between the semaphorin and the cleavable moiety, the semaphorin can be released from the chromatographic column by treatment with an appropriate enzyme or agent that specifically cleaves the fusion protein at this site [e.g., see Booth et al., Immunol. Lett. 19:65-70 (1988); and Gardella et al., J. Biol. Chem. 265:15854-15859 (1990)].

The semaphorin of the present invention is preferably retrieved in “substantially pure” form.

As used herein, the phrase “substantially pure” refers to a purity that allows for the effective use of the semaphorin in the applications described herein.

In addition to being synthesizable in host cells, the semaphorin of the present invention can also be synthesized using in vitro expression systems. These methods are well known in the art and the components of the system are commercially available.

As mentioned, the semaphorin may be administered to the subject in need thereof as polynucleotides where they are expressed in vivo i.e. gene therapy.

The phrase “gene therapy” as used herein refers to the transfer of genetic material (e.g. DNA or RNA) of interest into a host to treat or prevent a genetic or acquired disease or condition or phenotype. The genetic material of interest encodes a product (e.g. a protein, polypeptide, peptide, functional RNA, antisense) whose production in vivo is desired. For example, the genetic material of interest can encode a hormone, receptor, enzyme, polypeptide or peptide of therapeutic value. For review see, in general, the text “Gene Therapy” (Advanced in Pharmacology 40, Academic Press, 1997).

Two basic approaches to gene therapy have evolved: (1) ex vivo and (2) in vivo gene therapy. In ex vivo gene therapy cells are removed from a patient, and while being cultured are treated in vitro. Generally, a functional replacement gene is introduced into the cell via an appropriate gene delivery vehicle/method (transfection, transduction, homologous recombination, etc.) and an expression system as needed and then the modified cells are expanded in culture and returned to the host/patient. These genetically reimplanted cells have been shown to express the transfected genetic material in situ. The cells may be autologous or non-autologous to the subject. Since non-autologous cells are likely to induce an immune reaction when administered to the body several approaches have been developed to reduce the likelihood of rejection of non-autologous cells. These include either suppressing the recipient immune system or encapsulating the non-autologous cells in immunoisolating, semipermeable membranes before transplantation.

In in vivo gene therapy, target cells are not removed from the subject rather the genetic material to be transferred is introduced into the cells of the recipient organism in situ, that is within the recipient. These genetically altered cells have been shown to express the transfected genetic material in situ.

To confer specificity, preferably the nucleic acid constructs used to express the semaphorins of the present invention comprise cell-specific promoter sequence elements.

Recombinant viral vectors are useful for in vivo expression of the semaphorins of the present invention since they offer advantages such as lateral infection and targeting specificity. Lateral infection is inherent in the life cycle of, for example, retrovirus and is the process by which a single infected cell produces many progeny virions that bud off and infect neighboring cells. The result is that a large area becomes rapidly infected, most of which was not initially infected by the original viral particles. This is in contrast to vertical-type of infection in which the infectious agent spreads only through daughter progeny. Viral vectors can also be produced that are unable to spread laterally. This characteristic can be useful if the desired purpose is to introduce a specified gene into only a localized number of targeted cells.

The present inventors have shown that as well as having a direct effect on tumor cells, semaphorins also affect angiogenesis by interacting with receptors on endothelial cells.

Thus, as well as treating cancer, the semaphorins of the present invention may also treat other angiogenesis related disorders.

Angiogenesis-related diseases include, but are not limited to, inflammatory, autoimmune, and infectious diseases; angiogenesis-dependent cancer, including, for example, solid tumors, blood born tumors such as leukemias, and tumor metastases; benign tumors, for example hemangiomas, acoustic neuromas, neurofibromas, trachomas, and pyogenic granulomas; rheumatoid arthritis; psoriasis; eczema; ocular angiogenic diseases, for example, diabetic retinopathy, retinopathy of prematurity, macular degeneration, corneal graft rejection, neovascular glaucoma, retrolental fibroplasia, rubeosis; Osler-Webber Syndrome; myocardial angiogenesis; plaque neovascularization; telangiectasia; hemophiliac joints; angiofibroma; and wound granulation. In addition, compositions of this invention can be used to treat diseases such as, but not limited to, intestinal adhesions, atherosclerosis, scleroderma, warts, and hypertrophic scars (i.e., keloids). Compositions of this invention may also be useful in the treatment of diseases that have angiogenesis as a pathologic consequence such as cat scratch disease (Rochele minalia quintosa), ulcers (Helobacter pylori), tuberculosis, and leprosy.

The semaphorins or polynucleotides encoding same may be administered to a subject per se or they may be part of a pharmaceutical composition.

As used herein a “pharmaceutical composition” refers to a preparation of one or more of the active ingredients described herein with other chemical components such as physiologically suitable carriers and excipients. The purpose of a pharmaceutical composition is to facilitate administration of a compound to an organism.

Herein the term “active ingredient” refers to the semaphorin accountable for the biological effect.

Hereinafter, the phrases “physiologically acceptable carrier” and “pharmaceutically acceptable carrier” which may be interchangeably used refer to a carrier or a diluent that does not cause significant irritation to an organism and does not abrogate the biological activity and properties of the administered compound. An adjuvant is included under these phrases.

Herein the term “excipient” refers to an inert substance added to a pharmaceutical composition to further facilitate administration of an active ingredient. Examples, without limitation, of excipients include calcium carbonate, calcium phosphate, various sugars and types of starch, cellulose derivatives, gelatin, vegetable oils and polyethylene glycols.

Techniques for formulation and administration of drugs may be found in “Remington's Pharmaceutical Sciences,” Mack Publishing Co., Easton, Pa., latest edition, which is incorporated herein by reference.

Suitable routes of administration may, for example, include oral, rectal, transmucosal, especially transnasal, intestinal or parenteral delivery, including intramuscular, subcutaneous and intramedullary injections as well as intrathecal, direct intraventricular, intracardiac, e.g., into the right or left ventricular cavity, into the common coronary artery, intravenous, inrtaperitoneal, intranasal, or intraocular injections.

Conventional approaches for drug delivery to the central nervous system (CNS) include: neurosurgical strategies (e.g., intracerebral injection or intracerebroventricular infusion); molecular manipulation of the agent (e.g., production of a chimeric fusion protein that comprises a transport peptide that has an affinity for an endothelial cell surface molecule in combination with an agent that is itself incapable of crossing the BBB) in an attempt to exploit one of the endogenous transport pathways of the BBB; pharmacological strategies designed to increase the lipid solubility of an agent (e.g., conjugation of water-soluble agents to lipid or cholesterol carriers); and the transitory disruption of the integrity of the BBB by hyperosmotic disruption (resulting from the infusion of a mannitol solution into the carotid artery or the use of a biologically active agent such as an angiotensin peptide). However, each of these strategies has limitations, such as the inherent risks associated with an invasive surgical procedure, a size limitation imposed by a limitation inherent in the endogenous transport systems, potentially undesirable biological side effects associated with the systemic administration of a chimeric molecule comprised of a carrier motif that could be active outside of the CNS, and the possible risk of brain damage within regions of the brain where the BBB is disrupted, which renders it a suboptimal delivery method.

Alternately, one may administer the pharmaceutical composition in a local rather than systemic manner, for example, via injection of the pharmaceutical composition directly into a tissue region of a patient.

Pharmaceutical compositions of the present invention may be manufactured by processes well known in the art, e.g., by means of conventional mixing, dissolving, granulating, dragee-making, levigating, emulsifying, encapsulating, entrapping or lyophilizing processes.

Pharmaceutical compositions for use in accordance with the present invention thus may be formulated in conventional manner using one or more physiologically acceptable carriers comprising excipients and auxiliaries, which facilitate processing of the active ingredients into preparations which, can be used pharmaceutically. Proper formulation is dependent upon the route of administration chosen. For injection, the active ingredients of the pharmaceutical composition may be formulated in aqueous solutions, preferably in physiologically compatible buffers such as Hank's solution, Ringer's solution, or physiological salt buffer. For transmucosal administration, penetrants appropriate to the barrier to be permeated are used in the formulation. Such penetrants are generally known in the art.

For oral administration, the pharmaceutical composition can be formulated readily by combining the active compounds with pharmaceutically acceptable carriers well known in the art. Such carriers enable the pharmaceutical composition to be formulated as tablets, pills, dragees, capsules, liquids, gels, syrups, slurries, suspensions, and the like, for oral ingestion by a patient. Pharmacological preparations for oral use can be made using a solid excipient, optionally grinding the resulting mixture, and processing the mixture of granules, after adding suitable auxiliaries if desired, to obtain tablets or dragee cores. Suitable excipients are, in particular, fillers such as sugars, including lactose, sucrose, mannitol, or sorbitol; cellulose preparations such as, for example, maize starch, wheat starch, rice starch, potato starch, gelatin, gum tragacanth, methyl cellulose, hydroxypropylmethyl-cellulose, sodium carbomethylcellulose; and/or physiologically acceptable polymers such as polyvinylpyrrolidone (PVP). If desired, disintegrating agents may be added, such as cross-linked polyvinyl pyrrolidone, agar, or alginic acid or a salt thereof such as sodium alginate.

Dragee cores are provided with suitable coatings. For this purpose, concentrated sugar solutions may be used which may optionally contain gum arabic, talc, polyvinyl pyrrolidone, carbopol gel, polyethylene glycol, titanium dioxide, lacquer solutions and suitable organic solvents or solvent mixtures. Dyestuffs or pigments may be added to the tablets or dragee coatings for identification or to characterize different combinations of active compound doses.

Pharmaceutical compositions which can be used orally, include push-fit capsules made of gelatin as well as soft, sealed capsules made of gelatin and a plasticizer, such as glycerol or sorbitol. The push-fit capsules may contain the active ingredients in admixture with filler such as lactose, binders such as starches, lubricants such as talc or magnesium stearate and, optionally, stabilizers. In soft capsules, the active ingredients may be dissolved or suspended in suitable liquids, such as fatty oils, liquid paraffin, or liquid polyethylene glycols. In addition, stabilizers may be added. All formulations for oral administration should be in dosages suitable for the chosen route of administration.

For buccal administration, the compositions may take the form of tablets or lozenges formulated in conventional manner

For administration by nasal inhalation, the active ingredients for use according to the present invention are conveniently delivered in the form of an aerosol spray presentation from a pressurized pack or a nebulizer with the use of a suitable propellant, e.g., dichlorodifluoromethane, trichlorofluoromethane, dichloro-tetrafluoroethane or carbon dioxide. In the case of a pressurized aerosol, the dosage unit may be determined by providing a valve to deliver a metered amount. Capsules and cartridges of, e.g., gelatin for use in a dispenser may be formulated containing a powder mix of the compound and a suitable powder base such as lactose or starch.

The pharmaceutical composition described herein may be formulated for parenteral administration, e.g., by bolus injection or continuous infusion. Formulations for injection may be presented in unit dosage form, e.g., in ampoules or in multidose containers with optionally, an added preservative. The compositions may be suspensions, solutions or emulsions in oily or aqueous vehicles, and may contain formulatory agents such as suspending, stabilizing and/or dispersing agents.

Pharmaceutical compositions for parenteral administration include aqueous solutions of the active preparation in water-soluble form. Additionally, suspensions of the active ingredients may be prepared as appropriate oily or water based injection suspensions. Suitable lipophilic solvents or vehicles include fatty oils such as sesame oil, or synthetic fatty acids esters such as ethyl oleate, triglycerides or liposomes. Aqueous injection suspensions may contain substances, which increase the viscosity of the suspension, such as sodium carboxymethyl cellulose, sorbitol or dextran. Optionally, the suspension may also contain suitable stabilizers or agents which increase the solubility of the active ingredients to allow for the preparation of highly concentrated solutions.

Alternatively, the active ingredient may be in powder form for constitution with a suitable vehicle, e.g., sterile, pyrogen-free water based solution, before use.

The pharmaceutical composition of the present invention may also be formulated in rectal compositions such as suppositories or retention enemas, using, e.g., conventional suppository bases such as cocoa butter or other glycerides.

Pharmaceutical compositions suitable for use in context of the present invention include compositions wherein the active ingredients are contained in an amount effective to achieve the intended purpose. More specifically, a therapeutically effective amount means an amount of active ingredients (semaphorins) effective to prevent, alleviate or ameliorate symptoms of a disorder (e.g., cancer) or prolong the survival of the subject being treated.

Determination of a therapeutically effective amount is well within the capability of those skilled in the art, especially in light of the detailed disclosure provided herein.

For any preparation used in the methods of the invention, the therapeutically effective amount or dose can be estimated initially from in vitro and cell culture assays. For example, a dose can be formulated in animal models to achieve a desired concentration or titer. Such information can be used to more accurately determine useful doses in humans.

Toxicity and therapeutic efficacy of the active ingredients described herein can be determined by standard pharmaceutical procedures in vitro, in cell cultures or experimental animals. The data obtained from these in vitro and cell culture assays and animal studies can be used in formulating a range of dosage for use in human. The dosage may vary depending upon the dosage form employed and the route of administration utilized. The exact formulation, route of administration and dosage can be chosen by the individual physician in view of the patient's condition. (See e.g., Fingl, et al., 1975, in “The Pharmacological Basis of Therapeutics”, Ch. 1 p. 1).

Dosage amount and interval may be adjusted individually to ensure levels of the active ingredient are sufficient to induce or suppress the biological effect (minimal effective concentration, MEC). The MEC will vary for each preparation, but can be estimated from in vitro data. Dosages necessary to achieve the MEC will depend on individual characteristics and route of administration. Detection assays can be used to determine plasma concentrations.

Depending on the severity and responsiveness of the condition to be treated, dosing can be of a single or a plurality of administrations, with course of treatment lasting from several days to several weeks or until cure is effected or diminution of the disease state is achieved.

The amount of a composition to be administered will, of course, be dependent on the subject being treated, the severity of the affliction, the manner of administration, the judgment of the prescribing physician, etc.

Compositions of the present invention may, if desired, be presented in a pack or dispenser device, such as an FDA approved kit, which may contain one or more unit dosage forms containing the active ingredient. The pack may, for example, comprise metal or plastic foil, such as a blister pack. The pack or dispenser device may be accompanied by instructions for administration. The pack or dispenser may also be accommodated by a notice associated with the container in a form prescribed by a governmental agency regulating the manufacture, use or sale of pharmaceuticals, which notice is reflective of approval by the agency of the form of the compositions or human or veterinary administration. Such notice, for example, may be of labeling approved by the U.S. Food and Drug Administration for prescription drugs or of an approved product insert. Compositions comprising a preparation of the invention formulated in a compatible pharmaceutical carrier may also be prepared, placed in an appropriate container, and labeled for treatment of an indicated condition, as is further detailed above.

As used herein the term “about” refers to ±10%

The terms “comprises”, “comprising”, “includes”, “including”, “having” and their conjugates mean “including but not limited to”.

The term “consisting of means “including and limited to”.

The term “consisting essentially of” means that the composition, method or structure may include additional ingredients, steps and/or parts, but only if the additional ingredients, steps and/or parts do not materially alter the basic and novel characteristics of the claimed composition, method or structure.

As used herein the term “method” refers to manners, means, techniques and procedures for accomplishing a given task including, but not limited to, those manners, means, techniques and procedures either known to, or readily developed from known manners, means, techniques and procedures by practitioners of the chemical, pharmacological, biological, biochemical and medical arts.

It is appreciated that certain features of the invention, which are, for clarity, described in the context of separate embodiments, may also be provided in combination in a single embodiment. Conversely, various features of the invention, which are, for brevity, described in the context of a single embodiment, may also be provided separately or in any suitable subcombination or as suitable in any other described embodiment of the invention. Certain features described in the context of various embodiments are not to be considered essential features of those embodiments, unless the embodiment is inoperative without those elements.

Various embodiments and aspects of the present invention as delineated hereinabove and as claimed in the claims section below find experimental support in the following examples.

EXAMPLES

Reference is now made to the following examples, which together with the above descriptions illustrate some embodiments of the invention in a non limiting fashion. Reference is now made to the following examples, which together with the above descriptions, illustrate the invention in a non limiting fashion.

Generally, the nomenclature used herein and the laboratory procedures utilized in the present invention include molecular, biochemical, microbiological and recombinant DNA techniques. Such techniques are thoroughly explained in the literature. See, for example, “Molecular Cloning: A laboratory Manual” Sambrook et al., (1989); “Current Protocols in Molecular Biology” Volumes I-III Ausubel, R. M., ed. (1994); Ausubel et al., “Current Protocols in Molecular Biology”, John Wiley and Sons, Baltimore, Md. (1989); Perbal, “A Practical Guide to Molecular Cloning”, John Wiley & Sons, New York (1988); Watson et al., “Recombinant DNA”, Scientific American Books, New York; Birren et al. (eds) “Genome Analysis: A Laboratory Manual Series”, Vols. 1-4, Cold Spring Harbor Laboratory Press, New York (1998); methodologies as set forth in U.S. Pat. Nos. 4,666,828; 4,683,202; 4,801,531; 5,192,659 and 5,272,057; “Cell Biology: A Laboratory Handbook”, Volumes I-III Cellis, J. E., ed. (1994); “Culture of Animal Cells—A Manual of Basic Technique” by Freshney, Wiley-Liss, N.Y. (1994), Third Edition; “Current Protocols in Immunology” Volumes I-III Coligan J. E., ed. (1994); Stites et al. (eds), “Basic and Clinical Immunology” (8th Edition), Appleton & Lange, Norwalk, Conn. (1994); Mishell and Shiigi (eds), “Selected Methods in Cellular Immunology”, W.H. Freeman and Co., New York (1980); available immunoassays are extensively described in the patent and scientific literature, see, for example, U.S. Pat. Nos. 3,791,932; 3,839,153; 3,850,752; 3,850,578; 3,853,987; 3,867,517; 3,879,262; 3,901,654; 3,935,074; 3,984,533; 3,996,345; 4,034,074; 4,098,876; 4,879,219; 5,011,771 and 5,281,521; “Oligonucleotide Synthesis” Gait, M. J., ed. (1984); “Nucleic Acid Hybridization” Hames, B. D., and Higgins S. J., eds. (1985); “Transcription and Translation” Hames, B. D., and Higgins S. J., eds. (1984); “Animal Cell Culture” Freshney, R. I., ed. (1986); “Immobilized Cells and Enzymes” IRL Press, (1986); “A Practical Guide to Molecular Cloning” Perbal, B., (1984) and “Methods in Enzymology” Vol. 1-317, Academic Press; “PCR Protocols: A Guide To Methods And Applications”, Academic Press, San Diego, Calif. (1990); Marshak et al., “Strategies for Protein Purification and Characterization—A Laboratory Course Manual” CSHL Press (1996); all of which are incorporated by reference as if fully set forth herein. Other general references are provided throughout this document. The procedures therein are believed to be well known in the art and are provided for the convenience of the reader. All the information contained therein is incorporated herein by reference.

Example 1 Class-3 Semaphorins Inhibit the Development of Breast Cancer Derived Tumors by Targeting Receptor Expressing Tumor Cells

Materials and Methods

Materials: Antibodies directed against β-actin, and against the myc and FLAG epitope tags as well as chemicals were from Sigma (St. Louis, Mich.). Media and sera for cell culture were from Biological-Industries Inc. (Kibbutz Beth-Haemek, Israel). Fugene-6 was obtained from Roche Ltd (Switzerland). Antibodies directed against npl and np2 were purchased from Santa-Cruz inc. (San-Diego, Calif.). The cDNAs encoding different semaphorins were cloned to the NSPI-CMV-MCS-myc-His lentiviral expression vector containing SV40 promoter driving Puromycin selection marker. Antibodies directed against CD-31 were from BD biosciences Pharmingen. The PerfectPure RNA reverse

PCR kit was from 5-Prime (Gaithersburg, Md.). Expression plasmids: The cDNAs of sema3A, sema3F and sema3E were sub-cloned into the NSPI-CMV-myc-his lentiviral expression vector. The sema3G cDNA was cloned from HUVEC mRNA using RT-PCR. The sema3D cDNA was cloned using RT-PCR from HUVEC cells treated with 30 ng/ml of VEGF for 6 hours. The cDNAs encoding sema3D and sema3G were also subcloned into the NSPI expression vector. cDNA's containing the myc epitope tag were added in frame upstream to the stop codon of sema3D, sema3E, sema3F and sema3G. A FLAG epitope tag was added upstream to the stop codon of sema3A as described [Guttman-Raviv et al., 2007, J. Biol. Chem. 282:26294-26305].

Generation of recombinant lentiviruses and letiviral mediated infection of cells: HEK293-T cells were seeded in 100 mm tissue culture dishes (2.5×10⁶ cells per dish). A day after seeding, the cells were co-transfected with the appropriate lentiviral expression plasmid (8 μg), with the packaging vector pCMVdR8.91 (5 μg), and with a plasmid encoding the vesicular stomatitis virus coat envelope pMD2-VSVG (2 μg) using Fugene-6 according to the instructions of the vendor. Conditioned medium containing infective lentiviral particles was collected 48 hours and 72 hours post transfection. Polybrene (8 μg/ml) was added to the conditioned medium and incubated 8 hours with the target cells.

Cell lines: Mycoplasma free MDA-MB-231, MDA-MB-435, MDA-MB-468 and MCF7 breast cancer derived cells were obtained from the ATCC. The cells were cultured in DMEM containing 4.5 mg/ml glucose supplemented with 10% FCS and antibiotics. HUVEC, PAE, HEK293 and HEK293-T cells were cultured as previously described [Kessler O. et al, 2004, Cancer Res. 64:1008-1015]. HUVEC were used between passages 3-7.

In-vivo tumor formation assays: Cells expressing semaphorins or control cells infected with empty lentiviral vectors were implanted (5×10⁶/mouse) into the mammary fat pads of 4-6 week old balb\c nu/nu female mice (Harlan laboratories). In most experiments we groups of 9 animals/experiment were used. The tumors were measured twice a week using a caliper. The tumor volume (V) was determined using the formula, V=0.52×A²×B in which A is the short diameter and B is the long one. When MDA-MB-231 tumors reached an average volume of 200-300 mm³, they were excised and weighted. Each experiment was repeated at least twice to confirm the results. Estrogen pellets were used in experiments in which the development of tumors from MCF-7 cells was determined as previously described [Akiri G et al., 2003, Cancer Res. 63:1657-1666].

Immunohistochemistry: Tumors were embedded in OCT and frozen in 2-methylbutane cooled by liquid nitrogen. They were then sectioned into 30 μm thick sections using a cryostat. Sections were blocked with cold acetone, and reacted with an antibody directed against the endothelial marker CD-31, counterstained with hematoxilin and photographed. Eight different microscopic fields derived from different sections of three different tumors were photographed. These photographs were taken from areas in which the density of blood vessels was highest (hot spot method) [Vermeulen, P. B., 1996, Eur. J. Cancer 32A:2474-2484]. The area of the blood vessels in fields of equal area was quantified using the Image Pro Plus software.

Western Blots: Cell lysates were prepared and the concentration of protein determined as previously described [Guttman-Raviv, 2007, J. Biol. Chem. 282:26294-26305]. In order to determine the concentration of secreted sema3s in conditioned mediums of the various cell lines, cells were seeded in 12 well dishes at a concentration of 2×10⁵ cells/well. The cells were incubated for 48 hours in 0.4 ml of serum-free medium. Aliquots of equal volume were analyzed by western blot analysis for the presence of sema3s using antibodies directed against the appropriate myc or FLAG epitope tags as previously described described [Guttman-Raviv, 2007, J. Biol. Chem. 282:26294-26305]. None of the expressed semaphorins affected the proliferation rate or the survival of the various cell lines (data not shown).

Proliferation assay: Tumor cells (10⁴ cells/well) were seeded in triplicate in 24 well dishes. Adherent cells were trypsinized and counted every 24 hours for 4 days, using a coulter counter. The data was plotted on a semi-log graph in which the slope of the graph represents the growth rate of the cell line.

Adhesion assay: In cell adhesion experiments uncoated 12 well cell culture dishes were used as well as non-adhesive 12 well dishes coated with fibronectin (5 μl/ml). Tumor cells (10⁵ cells/well) were seeded in triplicates in growth media. The cells were washed twice with PBS, trypsinized to release adherent cells, and counted with a coulter counter. The cells were counted 5, 10, 20 and 45 minutes after they were seeded. The percentage of adherent cells relative to the number of seeded cells was then calculated and plotted. The time required for the adherence of 50% of the seeded cells was used as a measure to compare the adhesive properties of control cells and of the semaphorin expressing cells.

Endothelial cells repulsion assay: Cell repulsion assays were performed essentially as described [Guttman-Raviv, 2007, J. Biol. Chem. 282:26294-26305].

Soft-agar colony formation assay: A first layer of agar containing 2 ml of 0.5% low melting agar (Bio-Rad) dissolved in growth media was poured into the wells of a 6 well cell culture dish and allowed to polymerize at 4° C. for 20 minutes. A second layer (1 ml) containing 0.3% of low melting agar dissolved on growth media containing cells (3×10³/ml) was placed on top of the first layer and allowed to set at 4° C. for 20 minutes. Growth medium (2 ml) was added on top of the second layer and the cells were incubated in a humidified incubator at 37° C. for 21 days with a twice a week change of medium. At the end of the experiment, colonies were stained for 1 hour with 0.005% crystal violet, and incubated with PBS overnight to remove excess crystal violet. The colonies were photographed and colonies with a diameter of 150 μm or more were counted using the Image-pro morphometric software.

Statistical analysis: Statistical analysis was performed using the upaired data with unequal variance student's T-test. Error bars represent the standard error of the mean. Statistical significance is presented in the following manner: *p<0.05, **p<0.01 and ***p<0.001.

Results

Expression patterns of class-3 semaphorin receptors in breast cancer derived cell lines: Semaphorins may affect the development of tumors by several mechanisms which include direct effects on the tumor cells, effects on angiogenesis and effects on stromal cells. In order to find out if the class-3 semaphorins sema3A, sema3D, sema3E, sema3F and sema3G can influence the formation of tumors from breast cancer cells by directly influencing tumor cell behavior, the present inventors first determined the expression patterns of known sema3s receptors in the cells. The different types of breast cancer derived cells differed in their expression of sema3 receptors. MDA-MB-231 cells express predominantly np1, a receptor for sema3A and sema3D, but very little np2 if at all. MDA-MB-435 cells on the other hand express predominantly np2, a receptor for sema3F and sema3G and very little if any np1. MCF-7 cells express np1 (although at lower levels as compared to the MDA-MB-231 cells) and do not express np2 (FIG. 1A).

Because of their short intracellular domains the neuropilins cannot transduce sema3 signals on their own and form complexes with plexins in which the plexins serve as the signal transducing elements. All four cell lines expressed plexA1 and all but the MDA-MB-468 cells also expressed plexA2. However, none of the breast cancer derived cell lines expressed plexA4 and only the MCF-7 cells expressed low levels of plexA3 (FIGS. 1B-C). The mRNA encoding sema3E receptor PlexD1 was expressed in MDA-MB-231 and MCF-7 while MDA-MB-435 cells expressed lower concentrations and MDA-MB-468 cells did not express at all (FIGS. 1B-C).

The effects of different sema3s on the development of tumors from MDA-MB-231, MDA-MB-435, MDA-MB-468 and MCF-7 breast cancer cells: In order to determine the effects of sema3A, sema3D, sema3E, sema3F and sema3G in the breast cancer cell lines, the full length cDNAs encoding the five semaphorins (or a control of empty expression vector) were expressed in the cells using lentiviral vectors carrying a selection marker that conveys resistance to puromycin. Pools of infected cells were selected and examined for semaphorin expression by western blot analysis using antibodies directed against epitope tags incorporated into the recombinant semaphorins. Sema3s contain conserved cleavage sites for furin like pro-protein convertases and in the case of sema3E the cleaved product possess pro-metastatic properties. However, there was only minimal cleavage of any of the recombinant semaphorins in MDA-MB-231 cells or in the MDA-MB-435 cells (data not shown). The MDA-MB-231 cells were subsequently implanted in the mammary fat pads of immune deficient mice, and allowed to develop into tumors. In the case of the MDA-MB-231 cells, all the semaphorins that were tested were efficiently expressed (FIGS. 2A, D, G and J). Expression of the np1 agonist sema3A inhibited almost completely the development of tumors from these cells (FIGS. 2B-C). Sema3D is an agonist for np1 and for np2. Sema3D inhibited tumor formation completely in one experiment (data not shown) and in another experiment inhibited strongly though not completely the development of tumors (FIGS. 2E-F). In contrast, the np2 agonist sema3G was not able to inhibit the development of tumors from MDA-MB-231 cells (FIGS. 2K-L). Expression of the np2 agonist sema3F on the other hand, inhibited significantly the development of tumors from these cells despite the lack of np2 receptors. The tumors that developed from the sema3F expressing MDA-MB-231 cells (FIG. 2C) appeared much less bloody than the control tumors suggesting that sema3F inhibited tumor angiogenesis (FIG. 2A). Expression of the PlexD1 agonist sema3E also inhibited significantly the development of tumors from MDA-MB-231 cells but the resulting tumors did not look starved of blood vessels (FIGS. 2G-I).

A different picture emerges when the effects of these semaphorins on the development of tumors from np2 expressing MDA-MB-435 cells are examined. When control cells are injected into the mammary fat pads of nu/nu balb/c mice they develop into small tumors that stop growing when they reach an average volume of 50-100 mm³ (FIGS. 3B, E and H). In contrast, there is no such limitation on the development of tumors from any of the other breast cancer derived cell lines used in this study. Expression of the np2 agonist sema3F inhibited significantly the development of tumors from these cells (FIGS. 3B and C) and the np2 agonist sema3G was an even stronger inhibitor (FIGS. 3H-I). In contrast, expression of the np1 specific sema3A did not inhibit the development of tumors from these cells (FIGS. 3B-C), while sema3D, a semaphorin that binds to both neuropilins, also inhibited their development significantly but less potently than sema3G (FIGS. 3E-F). MDA-MB-435 cells also express the sema3E receptor PlexD1, although at a lower expression levels than those found in MDA-MB-231 cells (FIGS. 1A-B). Expression of sema3E did not inhibit the formation of tumors from the MDA-MB-435 cells. This was not due to cleavage by furin like pro-protein convertases since less than 5% of the sema3E found in the conditioned medium of these cells was cleaved (data not shown).

The present inventors also determined how the expression of sema3A and sema3F, the best studied np1 and np2 agonists respectively, affects the development of tumors from non-metastatic, estrogen dependent MCF-7 cells which express predominantly np1. Expression of sema3A inhibited significantly though not completely the development of tumors from these cells while sema3F did not (FIGS. 4A-C). These effects are similar to those observed with regard to the effect of these semaphorins on the development of tumors from MDA-MB-231 cells (FIGS. 2A and 2C). Taken together, these results suggest that sema3s ability to inhibit tumor formation from a given breast cancer derived cell type depends on the identity of the semaphorin receptors expressed by the cells of the developing tumor, and further suggest that sema3s should not be able to inhibit the formation of tumors from breast cancer cells that do not express sema3 receptors.

To put this prediction to the test, sema3A and sema3F were expressed in MDA-MB-468 breast cancer cells, which do not express np1, np2 or PlexD1 (FIG. 1A, C). These cells form slowly growing tumors upon injection into the mammary fat pads of nu/nu balb/c mice. In agreement with the present prediction, neither the expression of sema3A nor expression of sema3F significantly inhibited the formation of tumors from these cells (FIGS. 4E-F).

The effects of different class-3 semaphorins on tumor angiogenesis: Sema3F was characterized in several studies as an inhibitor of tumor angiogenesis and as a repulsive factor for endothelial cells and sema3A was also found to function as an inhibitor of VEGF induced angiogenesis and as a repulsive factor for endothelial cells although not as an inhibitor of tumor angiogenesis. To compare the repulsive properties of the different class-3 semaphorins HEK293 cells expressing similar levels of semaphorins were seeded on top of monolayers of human umbilical vein derived endothelial (HUVEC) cells at clonal densities. The HEK293 cells secreted similar concentrations of semaphorin into their growth media as determined by western blot analysis using antibodies directed against myc epitope tags that were fused in frame before the stop codon of the cDNAs of the different semaphorins (data not shown). Control cells infected with the empty lentiviral vector did not repel the endothelial cells but sema3A, sema3D and sema3E expressing cells repelled the endothelial cells efficiently (FIG. 5A). However, the np2 agonists sema3F and in particular sema3G repelled HUVEC less potently than the np1 agonists or the PlexD1 agonist sema3E (data not shown). Therefore cells expressing either sema3F or sema3G were seeded on top of porcine aortic endothelial (PAE) cells engineered to co-express np2 and plexA1. These cells were repelled very strongly by sema3F as expected but were still repelled rather inefficiently by sema3G (FIG. 5B).

In order to find out if the various sema3s that were examined in the present example inhibit tumor angiogenesis, the concentration of blood vessels in tumors that developed from control and semaphorin expressing breast cancer derived cells was determined. Since sema3A inhibited tumor formation in MDA-MB-231 cell almost completely it was not possible to determine the concentration of blood vessels in this case. However, expression of the np1 agonist sema3D in this cell type resulted in the formation of tumors containing significantly lower concentrations of blood vessels than in tumors that developed from control cells (FIG. 5C). The reduction in the concentration of tumor associated blood vessels was not correlated with the types of semaphorin receptors expressed by the cancer cells since expression of the np2 agonists sema3F and sema3G also reduced significantly the concentration of tumor associated blood vessels in tumors developing from MDA-MB-231 cells (FIG. 5C). Quantitatively, a similar reduction in the concentration of tumor associated blood vessels was observed regardless of whether sema3D or sema3G were used, even though sema3D expression inhibited tumor formation efficiently while sema3G did not inhibit tumor formation (FIGS. 2A-L). In-contrast, expression of sema3E, a semaphorin which inhibited the development of tumors from MDA-MB-231 cells (FIGS. 2G-I) and which inhibits the invasion of blood vessels into somites during early development, did not result in a decrease in the concentration of tumor associated blood vessels in MDA-MB-231 derived tumors (FIG. 5C).

The effects of sema3A and sema3F expression on the concentration of tumor associated blood vessels in MCF-7 cells were also examined. These tumors develop in the mammary fat pads of the mice only in the presence of slow estrogen release pellets. Expression of sema3A in these cells consistently and significantly reduced the concentration of tumor associated blood vessels. However, expression of sema3F did not (FIG. 5D).

In the case of the tumors that developed from the MDA-MB-435 cells, the expression of sema3A and sema3D was found to strongly reduce the concentration of blood vessels in resulting tumors (FIG. 5E) even though tumor development from these cells was not inhibited by these semaphorins (FIGS. 3A-I). It was not possible to determine the blood vessel concentration in tumors that developed from cells expressing sema3F or sema3G since the resulting tumors were too small or non-existent as in the case of sema3G. Expression of sema3E did produce a decrease in the concentration of blood vessels in tumors developing from these cells, but the decrease, although statistically significant, was small.

Taken together, these experiments indicate that although most of the semaphorins are able to inhibit angiogenesis, as manifested by the reduction in the concentration of blood vessels in tumors, and even though the inhibition may contribute to the inhibition of tumor progression, there was generally no correlation between this ability and the inhibition of tumor development which was mostly correlated with the expression of the appropriate semaphorin receptors by the tumor cells.

The effects of the expression of different class-3 semaphorins on the behavior of the tumor cells in-vitro: The experiments described hereinabove suggest that semaphorin expression may strongly modulate the behavior of tumor cells. Indeed, other researchers have described effects of various class-3 semaphorins on the adhesion, spreading and proliferation of various types of tumor cells [Tomizawa, Y., et al., 2001, Proc. Natl. Acad. Sci. U.S. A 98:13954-13959; Bielenberg, D. R., et al., 2004, J. Clin. Invest 114:1260-1271; Nasarre, P et al., 2005, Neoplasia. 7:180-189]. However, the proliferation of MDA-MB-231 cells expressing either sema3A, sema3F, sema3D or sema3E was not inhibited as compared to control cells infected with empty vector containing lentiviruses. Similarly, the proliferation of MCF-7 cells expressing either sema3A or sema3F was not altered as compared to controls and MDA-MB-435 cells expressing sema3A or sema3F were also not affected as compared to control cells (data not shown). These results indicate that the effect that these semaphorins have on the growth of tumors in-vivo are probably not mediated by a direct effect on the proliferation machinery of the tumor cells. The effect of the expression of different semaphorins on the adhesion of the various tumor cells to plastic or to fibronectin was also examined. Neither sema3A nor sema3F expression affected the rate or extent of adhesion of MDA-MB-231, MDA-MB-435 or MCF-7 cells regardless of whether the substrate was plastic or fibronectin (data not shown).

The ability to form colonies in soft-agar is a hallmark that differentiates many types of cancer cells from their normal counterparts. Therefore, the present inventors determined whether the expression of different class-3 semaphorins in MDA-MB-231 or MDA-MB-435 cells affects their ability to form colonies in soft-agar. None of the semaphorins inhibited completely the formation of colonies by MDA-MB-231 cells. However, both sema3A and sema3D, semaphorins that strongly inhibit tumor formation from these cells (FIGS. 2A-L), also significantly inhibited the formation of large colonies in soft agar (FIGS. 6A-B). Surprisingly, sema3F also inhibited significantly the formation of large colonies in soft agar despite the absence of np2 receptors on these cells. However, sema3F does bind to npl, albeit with a 10 fold lower affinity, and it is possible that this inhibitory effect is mediated by npl. Another np2 agonist, sema3G, which in contrast to sema3F does not inhibit the development of tumors from MDA-MB-231 cells at all (FIGS. 2J-L) and does not bind to npl, had no effect on the development of colonies in soft agar (FIGS. 6A-B). These results suggested that the semaphorin needs to bind to the semaphorin receptor expressed by the tumor cells in order to be able to inhibit soft-agar colony formation. MDA-MB-231 cells also express the sema3E receptor PlexD1 and expression of sema3E inhibits the formation of tumor formation from these cells (FIGS. 2G-I). However, sema3E failed to inhibit the formation of large colonies of MDA-MB-231 cells in soft-agar (FIGS. 6A-B).

Based on these results the present inventors predicted that sema3D, sema3F and sema3G, which inhibit tumor formation from MDA-MB-435 cells (FIGS. 3A-I), should also inhibit efficiently the formation of soft-agar colonies from these np2 expressing cells. Indeed, sema3d and sema3G inhibited colony formation efficiently as predicted. However, unexpectedly it was found that sema3F inhibited the formation of colonies in soft agar from these cells even though it did not inhibit the formation of tumors from these cells (FIGS. 6C-D). Another unexpected observation was that sema3E, which did not inhibit the formation of tumors from these cells did inhibit colony formation (FIGS. 6C-D). Lastly, it was expected that sema3A would not affect colony formation since its receptor is not expressed by MDA-MB-435 cells (FIGS. 10A-C). Indeed, colony formation from MDA-MB-435 cells was not inhibited by sema3A. Instead it was even enhanced (FIGS. 6C-D).

Taken together these results suggest that the different semaphorins are able to modulate the behavior of MDA-MB-231 and MDA-MB-435 cells directly, although there were exceptions to this rule.

Expression of np1 in MDA-MB-435 cells enhances tumor development and the enhancement is negated by co-expression of sema3A: The experiments described above suggest that the expression of specific class-3 semaphorin receptors by breast cancer derived tumor cells is probably the most important factor that determines whether a given class-3 semaphorin will be an effective inhibitor of tumor development. To test this hypothesis the present inventors asked whether expression of npl in MDA-MB-435 cells would render tumors that will develop from these cells sensitive to sema3A. Tumors that developed from MDA-MB-435 cells that express np1 did not stop developing when they reached a mean volume of 50-100 mm³ like wild-type MDA-MB-435 cells (FIGS. 3A-I). The np1 expressing MDA-MB-435 cells formed rapidly forming tumors when implanted in the mammary fat pads of mice (FIGS. 7A-C). Even though these np1 expressing cells formed tumors that appeared bloody, the concentration of blood vessels within these tumors, as determined by staining with an antibody directed against CD-31, was not significantly different from that of control tumors (FIG. 7D). When the np1 agonist sema3A was co-expressed in these cells with npl, the cells that expressed both genes reverted to the behavior exhibited by the parental cells and formed tumors that stopped growing when the tumors reached a volume of 50-100 mm³ thereby eliminating the growth advantage conferred by the presence of np1 (FIGS. 7A-C), but not that conferred by the presence of np2 which can be inhibited by np2 agonists such as sema3F or sema3G (FIGS. 3A-I). Interestingly, the density of blood vessels in tumors that developed from MDA-MB-435 cells expressing sema3A or sema3A+np1 was similar and significantly lower than in tumors that developed from MDA-MB-435 cells that do not express sema3A (FIG. 7D), suggesting once again that inhibition of angiogenesis represents part of the mechanism by which semaphorins modulate tumor progression, but that it may not always be sufficient to inhibit tumor expansion.

Discussion

The present results indicate for the first time that sema3A, sema3D, sema3E and sema3G inhibit the formation of tumors from several cell lines derived from human breast carcinomas. It should be noted that sema3E was previously described as a pro-metastatic agent, but the pro-metastatic activity was associated with a cleavage product generated by furin like pro-protein convertases and not by the full length protein. In the present experiments there was almost no cleavage of sema3E in the MDA-MB-231 cells or MDA-MB-435 cells.

Many types of tumorigenic cells express one or more than one of the class-3 semaphorin receptors np1, np2 or PlexD1. The breast cancer derived cell types that were employed in the present examples in order to study the anti-tumorigenic effects of the different semaphorins, express different combinations of class-3 semaphorin receptors on their cell surfaces. Both neuropilins as well as several types of plexins are also expressed in endothelial cells in which they play an important role in the transduction of VEGF induced angiogenic signals, and mediate the anti-angiogenic effects of sema3s. In the present study the present inventors have tried to evaluate the relative importance of the anti-angiogenic effects versus the direct effects of the sema3s in the determination of the anti-tumorigenic properties of different sema3s. Taken together, the present examples indicate that the expression of a given semaphorin receptor by the tumorigenic cells is probably the most important factor which determines whether a given class-3 semaphorin will function as an effective inhibitor of tumor development. Thus, the development of tumors from MDA-MB-231 cells that express np1 but not np2 is strongly inhibited by the np1 agonists sema3A and sema3D but not by the np2 agonist sema3G. This conclusion is also supported by experiments which have shown that in the case of the np2 expressing MDA-MB-435 cells sema3A does not inhibit tumor development and sema3D inhibits tumor development weakly while sema3G and sema3F function in the case of these cells as very effective inhibitors. Furthermore, neither sema3A nor sema3F were able to inhibit the development of tumors from MDA-MB-468 cell that do not express neuropilins.

Sema3E is unique among sema3s as it is the only semaphorin which does not bind to neuropilins and instead activates directly PlexD1. Both MDA-MB-231 and MDA-MB-435 cells express PlexD1 although the expression levels in MDA-MB-435 cells are significantly lower than in MDA-MB-231 cells. Sema3E inhibited significantly tumor development from MDA-MB-231 cells but not at all from MDA-MB-435 cells. It is possible that the levels of expression of PlexD1 in the MDA-MB-435 cells are below a critical threshold that does not enable inhibition of tumor development by sema3E. Thus, this result may perhaps also be regarded as one that supports the above mentioned rule of thumb. PlexD1 can form complexes with neuropilins, and at least in the case of np1 this interaction can affect the nature of the biological response to sema3E. It is therefore possible that in the MDA-MB-435 cells, the effect of sema3E may be inhibited by np2 while in MDA-MB-231 cells np1 may affect sema3E signaling differently, resulting in diverse biological responses.

The present inventors showed for the first time that sema3D, sema3G, sema3A and sema3E function as inhibitors of tumor angiogenesis since their expression in tumor cells resulted in a significant reduction in the density of tumor associated blood vessels. These results indicate that as a rule, semaphorin expression tends to reduce the density of blood vessels in tumors that develop from MDA-MB-231, MDA-MB-435 or MCF-7 cells even in cases in which tumor development is not inhibited by the given semaphorin. However, there were a few exceptions to this rule. The density of blood vessels in tumors derived from sema3F expressing MCF-7 cells was not reduced in comparison with tumors derived from control MCF-7 cells. However, the development of tumors from MCF-7 cells requires estrogen, a hormone that was recently found to inhibit the expression of the sema3F receptor np2, which may perhaps explain the lack of the anti-angiogenic effect in this case. In addition it was found that expression of sema3E in MDA-MB-231 cells also failed to reduce the density of blood vessels in resulting tumors in spite of significant inhibition of tumor growth.

The density of tumor associated blood vessels is determined by a balance between the rate of tumor angiogenesis, which tends to increase blood vessel density, and the rate of tumor cell proliferation which tends to decrease it. It is therefore possible that a small tumor whose expansion was strongly inhibited by an anti-angiogenic agent will contain the same density of blood vessels as a tumor whose expansion was much less affected by the anti-angiogenic agent, simply because in the latter case the reduction in the density of blood vessels did not reach that threshold below which the expansion of the tumor mass is inhibited. It was observed that in most cases the expression of class-3 semaphorins by the tumor cells reduces the density of blood vessels in resulting tumors, regardless of the receptor types with which the specific semaphorins interact and regardless of whether the sema3s were able to inhibit the development of the tumors. For example, sema3G decreased significantly the density of blood vessels in tumors derived from MDA-MB-231 cells as did sema3D and sema3F even though in contrast with these semaphorins sema3G did not inhibit tumor development.

The present inventors reasoned that if the expression of semaphorin receptors by the tumor cells is the primary factor that determines whether sema3s will be able to inhibit tumor development, than the expression of semaphorins should affect the behavior of such tumor cells in in-vitro assays too. Class-3 semaphorins such as sema3F and sema3B inhibit the adhesion and migration of some tumor cells. It was therefore surprising that neither the proliferation, nor the adhesive properties of the different tumor cells used in this study were modified the expression of the different semaphorins. So far, the only property of the tumor cells which was found to be affected by the expression of semaphorins was their ability to form colonies in soft-agar. In general, semaphorins that inhibited the formation of tumors from either MDA-MB-231 or MDA-MB-435 cells were also able to inhibit the anchorage independent growth of the tumor cells. Anchorage independent growth is a hallmark of most malignant cells and these observations indicate that the sema3s directly influence a tumor cell characteristic that is correlated with their malignant properties. However, a few exceptions to this rule were also noticed. Expression of sema3E in MDA-MB-231 cells did not inhibit the anchorage free growth of the cells even though the formation of tumors from these cells was inhibited. Another discrepancy was noted in the case of sema3F, which when expressed in MDA-MB-435 cells inhibited strongly tumor formation but not the anchorage free growth of these cells. The reason for these discrepancies is still under investigation, but nevertheless, in general there is good agreement between the effects of the sema3s on the development of the tumors and their ability to inhibit anchorage free growth.

In conclusion, the present inventors have found for the first time that sema3A, sema3D, sema3E and sema3G possess anti-tumorigenic properties similar to those displayed by the previously identified tumor suppressors sema3F and sema3B. It was also found that all of these semaphorins can repulse endothelial cells with varying potencies and that all of them are able to significantly reduce the density of blood vessels in tumors that develop from tumor cells expressing these semaphorins. Sema3E was an exception since even though it functioned as a potent repulsive agent for endothelial cells in-vitro, it had no effect on the density of blood vessels in tumors that developed from MDA-MB-231 cells and only a small effect on the density of blood vessels in tumors that develop from MDA-MB-435 cells. In addition, a strong correlation between the ability to inhibit tumor growth in-vivo and the ability to inhibit anchorage independent growth in-vitro by individual semaphorins was noted. These observations lead to the conclusion that efficient inhibition of tumor development by semaphorins is enabled when an individual semaphorin is able to inhibit directly the malignant properties of the tumor cells and when this semaphorin is also able to efficiently inhibit tumor angiogenesis. The present results argue that semaphorins may find use as general anti-angiogenic agents. However, for maximal effectiveness as anti-tumorigenic agents the selection of specific semaphorins or semaphorin combinations will have to take into account the identity of the semaphorin receptors expressed by the tumorigenic cells of target tumors.

Although the invention has been described in conjunction with specific embodiments thereof, it is evident that many alternatives, modifications and variations will be apparent to those skilled in the art. Accordingly, it is intended to embrace all such alternatives, modifications and variations that fall within the spirit and broad scope of the appended claims.

All publications, patents and patent applications mentioned in this specification are herein incorporated in their entirety by into the specification, to the same extent as if each individual publication, patent or patent application was specifically and individually indicated to be incorporated herein by reference. In addition, citation or identification of any reference in this application shall not be construed as an admission that such reference is available as prior art to the present invention. To the extent that section headings are used, they should not be construed as necessarily limiting. 

1. A method of treating cancer in a subject in need thereof, the method comprising: (a) determining an expression of PlexD1 receptor on cells of a tumor sample of the subject; and (b) when an amount of said PlexD1 receptor is above a predetermined threshold, contacting cancerous cells of the subject with a therapeutically effective amount of pro-protein convertase resistant Semaphorin 3E thereby treating the cancer.
 2. The method of claim 1, wherein said contacting is effected by systemic administration.
 3. The method of claim 1, wherein said contacting is effected by local administration.
 4. The method of claim 1, wherein said cancer is selected from the group consisting of breast cancer, pancreatic cancer and lung cancer.
 5. The method of claim 1, wherein said detecting is effected using an antibody which is capable of identifying said PlexD1 receptor.
 6. A method of treating cancer in a subject in need thereof comprising administering to the subject a therapeutically effective amount of a pro-protein convertase resistant semaphorin 3E, thereby treating the cancer.
 7. The method of claim 6, wherein said administering comprises systemic administration.
 8. The method of claim 6, wherein said administering comprises local administration.
 9. The method of claim 6, wherein said cancer is selected from the group consisting of breast cancer, pancreatic cancer and lung cancer. 